HEADER OXYGEN STORAGE 27-FEB-92 1MYJ TITLE DISTAL POLARITY IN LIGAND BINDING TO MYOGLOBIN: STRUCTURAL TITLE 2 AND FUNCTIONAL CHARACTERIZATION OF A THREONINE68(E11) TITLE 3 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA KEYWDS OXYGEN STORAGE EXPDTA X-RAY DIFFRACTION AUTHOR S.J.SMERDON,T.J.OLDFIELD,A.J.WILKINSON,Z.DAUTER,K.PETRATOS, AUTHOR 2 K.S.WILSON REVDAT 3 01-APR-03 1MYJ 1 JRNL REVDAT 2 30-JAN-94 1MYJ 3 REMARK FTNOTE HETATM REVDAT 1 31-JAN-94 1MYJ 0 JRNL AUTH S.J.SMERDON,G.G.DODSON,A.J.WILKINSON,Q.H.GIBSON, JRNL AUTH 2 R.S.BLACKMORE,T.E.CARVER,J.S.OLSON JRNL TITL DISTAL POCKET POLARITY IN LIGAND BINDING TO JRNL TITL 2 MYOGLOBIN: STRUCTURAL AND FUNCTIONAL JRNL TITL 3 CHARACTERIZATION OF A THREONINE68(E11) MUTANT. JRNL REF BIOCHEMISTRY V. 30 6252 1991 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.J.SMERDON,T.J.OLDFIELD,E.J.DODSON,G.G.DODSON, REMARK 1 AUTH 2 R.E.HUBBARD,A.J.WILKINSON REMARK 1 TITL DETERMINATION OF THE CRYSTAL STRUCTURE OF REMARK 1 TITL 2 RECOMBINANT PIG MYOGLOBIN BY MOLECULAR REPLACEMENT REMARK 1 TITL 3 AND ITS REFINEMENT REMARK 1 REF ACTA CRYSTALLOGR.,SECT.B V. 46 370 1990 REMARK 1 REFN ASTM ACBCAR DK ISSN 0567-7408 REMARK 1 REFERENCE 2 REMARK 1 AUTH G.G.DODSON,R.E.HUBBARD,T.J.OLDFIELD,S.J.SMERDON, REMARK 1 AUTH 2 A.J.WILKINSON REMARK 1 TITL APOMYOGLOBIN AS A MOLECULAR RECOGNITION SURFACE: REMARK 1 TITL 2 EXPRESSION, RECONSTITUTION AND CRYSTALLISATION OF REMARK 1 TITL 3 RECOMBINANT PORCINE MYOGLOBIN IN ESCHERICHIA COLI REMARK 1 REF PROTEIN ENG. V. 2 233 1988 REMARK 1 REFN ASTM PRENE9 UK ISSN 0269-2139 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 35296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2394 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.027 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.072 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.084 ; 0.060 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.016 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.152 ; 0.120 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.222 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.324 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.186 ; 0.500 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 3.292 ; 20.000 REMARK 3 STAGGERED (DEGREES) : 21.510; 20.000 REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.393 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.304 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.135 ; 1.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.059 ; 2.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MYJ COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-17) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,1/2+Y,-Z REMARK 290 3555 1/2+X,1/2+Y,1/2+Z REMARK 290 4555 1/2-X,Y,1/2-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 21.24000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 60.22861 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.24000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.99554 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.22861 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 45.99554 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMOLECULE: 2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O HOH 60 O HOH 61 1.80 REMARK 500 OE1 GLN B 26 O HOH 1 1.85 REMARK 500 FE HEM A 154 O HOH 57 1.95 REMARK 500 O HOH 39 O HOH 91 2.02 REMARK 500 FE HEM B 154 O HOH 72 2.10 REMARK 500 O HOH 3 O HOH 68 2.10 REMARK 500 NE2 HIS B 93 FE HEM B 154 2.12 REMARK 500 NE2 HIS A 93 FE HEM A 154 2.14 REMARK 500 OE1 GLN A 8 OD1 ASN A 12 2.17 REMARK 500 NE2 GLN A 26 O HOH 22 2.18 REMARK 500 O HOH 16 O HOH 51 2.18 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS B 34 CA - CB - CG ANGL. DEV. = 55.1 DEGREES REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 152 2.38 110.88 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 10 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH 17 DISTANCE = 7.20 ANGSTROMS REMARK 525 HOH 90 DISTANCE = 5.73 ANGSTROMS DBREF 1MYJ A 1 153 UNP P02189 MYG_PIG 1 153 DBREF 1MYJ B 1 153 UNP P02189 MYG_PIG 1 153 SEQADV 1MYJ THR A 68 UNP P02189 VAL 68 CONFLICT SEQADV 1MYJ THR B 68 UNP P02189 VAL 68 CONFLICT SEQRES 1 A 153 GLY LEU SER ASP GLY GLU TRP GLN LEU VAL LEU ASN VAL SEQRES 2 A 153 TRP GLY LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY GLN SEQRES 3 A 153 GLU VAL LEU ILE ARG LEU PHE LYS GLY HIS PRO GLU THR SEQRES 4 A 153 LEU GLU LYS PHE ASP LYS PHE LYS HIS LEU LYS SER GLU SEQRES 5 A 153 ASP GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS GLY SEQRES 6 A 153 ASN THR THR LEU THR ALA LEU GLY GLY ILE LEU LYS LYS SEQRES 7 A 153 LYS GLY HIS HIS GLU ALA GLU LEU THR PRO LEU ALA GLN SEQRES 8 A 153 SER HIS ALA THR LYS HIS LYS ILE PRO VAL LYS TYR LEU SEQRES 9 A 153 GLU PHE ILE SER GLU ALA ILE ILE GLN VAL LEU GLN SER SEQRES 10 A 153 LYS HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 153 MET SER LYS ALA LEU GLU LEU PHE ARG ASN ASP MET ALA SEQRES 12 A 153 ALA LYS TYR LYS GLU LEU GLY PHE GLN GLY SEQRES 1 B 153 GLY LEU SER ASP GLY GLU TRP GLN LEU VAL LEU ASN VAL SEQRES 2 B 153 TRP GLY LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY GLN SEQRES 3 B 153 GLU VAL LEU ILE ARG LEU PHE LYS GLY HIS PRO GLU THR SEQRES 4 B 153 LEU GLU LYS PHE ASP LYS PHE LYS HIS LEU LYS SER GLU SEQRES 5 B 153 ASP GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS GLY SEQRES 6 B 153 ASN THR THR LEU THR ALA LEU GLY GLY ILE LEU LYS LYS SEQRES 7 B 153 LYS GLY HIS HIS GLU ALA GLU LEU THR PRO LEU ALA GLN SEQRES 8 B 153 SER HIS ALA THR LYS HIS LYS ILE PRO VAL LYS TYR LEU SEQRES 9 B 153 GLU PHE ILE SER GLU ALA ILE ILE GLN VAL LEU GLN SER SEQRES 10 B 153 LYS HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 B 153 MET SER LYS ALA LEU GLU LEU PHE ARG ASN ASP MET ALA SEQRES 12 B 153 ALA LYS TYR LYS GLU LEU GLY PHE GLN GLY FTNOTE 1 RESIDUES 152 AND 153 ARE DISORDERED AND NOT DEFINED IN FTNOTE 1 DENSITY MAPS. FTNOTE 2 HOH 57 AND 72 ARE WATER MOLECULES IN THE HAEM POCKET AND FTNOTE 2 LIGATED TO THE HAEM IRON. HET SO4 1 5 HET SO4 2 5 HET HEM A 154 43 HET HEM B 154 43 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HEM 2(C34 H32 FE N4 O4) FORMUL 7 HOH *107(H2 O) HELIX 1 A1 SER A 3 GLU A 18 1 16 HELIX 2 B1 ASP A 20 GLY A 35 1 16 HELIX 3 C1 HIS A 36 LYS A 42 1 7 HELIX 4 D1 SER A 51 ALA A 57 1 7 HELIX 5 E1 SER A 58 LYS A 77 1 20 HELIX 6 F1 LEU A 86 THR A 95 1 10 HELIX 7 G1 PRO A 100 LYS A 118 1 19 HELIX 8 H1 GLY A 124 LEU A 149 1 26 HELIX 9 A2 SER B 3 GLU B 18 1 16 HELIX 10 B2 ASP B 20 GLY B 35 1 16 HELIX 11 C2 HIS B 36 LYS B 42 1 7 HELIX 12 D2 SER B 51 ALA B 57 1 7 HELIX 13 E2 SER B 58 LYS B 77 1 20 HELIX 14 F2 LEU B 86 THR B 95 1 10 HELIX 15 G2 PRO B 100 LYS B 118 1 19 HELIX 16 H2 GLY B 124 LEU B 149 1 26 CRYST1 123.750 42.480 92.050 90.00 92.05 90.00 I 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008081 0.000000 0.000289 0.00000 SCALE2 0.000000 0.023540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010871 0.00000