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HEADER OXYGEN STORAGE 20-JUL-93 2FAM TITLE X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA TITLE 2 MYOGLOBIN IN DIFFERENT LIGANDED STATES COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: APLYSIA LIMACINA KEYWDS OXYGEN STORAGE EXPDTA X-RAY DIFFRACTION AUTHOR E.CONTI,C.MOSER,M.RIZZI,A.MATTEVI,C.LIONETTI,A.CODA, AUTHOR 2 P.ASCENZI,M.BRUNORI,M.BOLOGNESI REVDAT 2 31-JAN-94 2FAM 1 REMARK REVDAT 1 31-OCT-93 2FAM 0 JRNL AUTH E.CONTI,C.MOSER,M.RIZZI,A.MATTEVI,C.LIONETTI, JRNL AUTH 2 A.CODA,P.ASCENZI,M.BRUNORI,M.BOLOGNESI JRNL TITL X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA JRNL TITL 2 MYOGLOBIN IN DIFFERENT LIGANDED STATES. JRNL REF J.MOL.BIOL. V. 233 498 1993 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.LIONETTI,M.G.GUANZIROLI,F.FRIGERIO,P.ASCENZI, REMARK 1 AUTH 2 M.BOLOGNESI REMARK 1 TITL X-RAY CRYSTAL STRUCTURE OF THE FERRIC SPERM WHALE REMARK 1 TITL 2 MYOGLOBIN: IMIDAZOLE COMPLEX AT 2.0 ANGSTROMS REMARK 1 TITL 3 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 217 409 1991 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.BOLOGNESI,F.FRIGERIO,C.LIONETTI,M.RIZZI, REMARK 1 AUTH 2 P.ASCENZI,M.BRUNORI REMARK 1 TITL APLYSIA LIMACINA MYOGLOBIN: MOLECULAR BASES FOR REMARK 1 TITL 2 LIGAND BINDING REMARK 1 EDIT S.N.VINOGRADOV, O.H.KAPP REMARK 1 REF STRUCTURE AND FUNCTION OF 161 1991 REMARK 1 REF 2 INVERTEBRATE OXYGEN CARRIERS REMARK 1 PUBL SPRINGER VERLAG, NEW YORK REMARK 1 REFN ISBN 0-387-97585-3 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.MATTEVI,G.GATTI,A.CODA,M.RIZZI,P.ASCENZI, REMARK 1 AUTH 2 M.BRUNORI,M.BOLOGNESI REMARK 1 TITL BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA REMARK 1 TITL 2 MYOGLOBIN: CRYSTALLOGRAPHIC ANALYSIS AT 1.9 REMARK 1 TITL 3 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.RECOG. V. 4 1 1991 REMARK 1 REFN ASTM JMORE4 UK ISSN 0952-3499 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.BOLOGNESI,A.CODA,F.FRIGERIO,G.GATTI,P.ASCENZI, REMARK 1 AUTH 2 M.BRUNORI REMARK 1 TITL X-RAY CRYSTAL STRUCTURE OF THE FLUORIDE DERIVATIVE REMARK 1 TITL 2 OF APLYSIA LIMACINA MYOGLOBIN AT 2.0 ANGSTROMS REMARK 1 TITL 3 RESOLUTION: STABILIZATION OF THE FLUORIDE BY REMARK 1 TITL 4 HYDROGEN BONDING TO ARG66 (E10) REMARK 1 REF J.MOL.BIOL. V. 213 621 1990 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 5 REMARK 1 AUTH M.BOLOGNESI,S.ONESTI,G.GATTI,A.CODA,P.ASCENZI, REMARK 1 AUTH 2 M.BRUNORI REMARK 1 TITL APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC REMARK 1 TITL 2 ANALYSIS AT 1.6 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 205 529 1989 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 6 REMARK 1 AUTH M.BOLOGNESI,E.CANNILLO,P.ASCENZI,G.M.GIACOMETTI, REMARK 1 AUTH 2 A.MERLI,M.BRUNORI REMARK 1 TITL REACTIVITY OF FERRIC APLYSIA AND SPERM WHALE REMARK 1 TITL 2 MYOGLOBINS TOWARDS IMIDAZOLE. X-RAY AND BINDING REMARK 1 TITL 3 STUDY REMARK 1 REF J.MOL.BIOL. V. 158 305 1982 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD :NULL REMARK 3 FREE R VALUE TEST SET SELECTION :NULL REMARK 3 R VALUE (WORKING + TEST SET) :0.161 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 USING ALL DATA, NO SIGMA CUTOFF. 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 : 1086 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.018 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.900 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FAM 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 (2007-03-23) 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 (%): 37.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 26.49000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.49000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.35000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 146 CG CD CE NZ 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 NE2 HIS A 95 FE HEM 148 2.01 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASN A 80 O HOH 203 4547 2.02 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 12 CE LYS A 12 NZ -0.131 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 156 DISTANCE = 5.36 ANGSTROMS REMARK 525 HOH 163 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH 165 DISTANCE = 5.60 ANGSTROMS REMARK 525 HOH 196 DISTANCE = 5.76 ANGSTROMS REMARK 525 HOH 199 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH 207 DISTANCE = 5.06 ANGSTROMS REMARK 525 HOH 210 DISTANCE = 5.07 ANGSTROMS REMARK 525 HOH 402 DISTANCE = 5.32 ANGSTROMS REMARK 525 HOH 412 DISTANCE = 5.25 ANGSTROMS REMARK 525 HOH 414 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH 415 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH 416 DISTANCE = 5.53 ANGSTROMS REMARK 525 HOH 419 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH 421 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH 424 DISTANCE = 6.47 ANGSTROMS DBREF 2FAM A 1 146 UNP P02210 GLB_APLLI 1 146 SEQADV 2FAM ASN A 22 UNP P02210 ASP 22 CONFLICT SEQADV 2FAM LEU A 26 UNP P02210 ASP 26 CONFLICT SEQADV 2FAM ASP A 27 UNP P02210 ALA 27 CONFLICT SEQADV 2FAM ASN A 80 UNP P02210 ASP 80 CONFLICT SEQRES 1 A 147 ACE SER LEU SER ALA ALA GLU ALA ASP LEU ALA GLY LYS SEQRES 2 A 147 SER TRP ALA PRO VAL PHE ALA ASN LYS ASN ALA ASN GLY SEQRES 3 A 147 LEU ASP PHE LEU VAL ALA LEU PHE GLU LYS PHE PRO ASP SEQRES 4 A 147 SER ALA ASN PHE PHE ALA ASP PHE LYS GLY LYS SER VAL SEQRES 5 A 147 ALA ASP ILE LYS ALA SER PRO LYS LEU ARG ASP VAL SER SEQRES 6 A 147 SER ARG ILE PHE THR ARG LEU ASN GLU PHE VAL ASN ASN SEQRES 7 A 147 ALA ALA ASN ALA GLY LYS MET SER ALA MET LEU SER GLN SEQRES 8 A 147 PHE ALA LYS GLU HIS VAL GLY PHE GLY VAL GLY SER ALA SEQRES 9 A 147 GLN PHE GLU ASN VAL ARG SER MET PHE PRO GLY PHE VAL SEQRES 10 A 147 ALA SER VAL ALA ALA PRO PRO ALA GLY ALA ASP ALA ALA SEQRES 11 A 147 TRP THR LYS LEU PHE GLY LEU ILE ILE ASP ALA LEU LYS SEQRES 12 A 147 ALA ALA GLY LYS HET ACE A 0 3 HET SCN 149 3 HET HEM 148 43 HETNAM ACE ACETYL GROUP HETNAM SCN THIOCYANATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 1 ACE C2 H4 O FORMUL 2 SCN C N S 1- FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *93(H2 O) HELIX 1 A ALA A 4 ALA A 19 1 16 HELIX 2 B LYS A 21 LYS A 35 1 15 HELIX 3 C PRO A 37 PHE A 42 5 6 HELIX 4 D VAL A 51 LYS A 55 1 5 HELIX 5 E LYS A 59 ASN A 76 1 18 HELIX 6 F ALA A 81 GLY A 97 1 17 HELIX 7 G SER A 102 SER A 118 1 17 HELIX 8 H ALA A 126 ALA A 143 1 18 LINK S SCN 149 FE HEM 148 CRYST1 52.980 70.700 32.500 90.00 90.00 90.00 P 21 21 21 4 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 0.018875 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014144 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030769 0.00000