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HEADER OXYGEN STORAGE 01-FEB-95 1LHS TITLE LOGGERHEAD SEA TURTLE MYOGLOBIN (AQUO-MET) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARETTA CARETTA KEYWDS OXYGEN STORAGE EXPDTA X-RAY DIFFRACTION AUTHOR M.NARDINI,C.TARRICONE,A.LANIA,A.DESIDERI,G.DE SANCTIS, AUTHOR 2 M.COLETTA,R.PETRUZZELLI,P.ASCENZI,A.CODA,M.BOLOGNESI REVDAT 2 01-APR-03 1LHS 1 JRNL REVDAT 1 03-JUN-95 1LHS 0 JRNL AUTH M.NARDINI,C.TARRICONE,M.RIZZI,A.LANIA,A.DESIDERI, JRNL AUTH 2 G.DE SANCTIS,M.COLETTA,R.PETRUZZELLI,P.ASCENZI, JRNL AUTH 3 A.CODA,ET AL. JRNL TITL REPTILE HEME PROTEIN STRUCTURE: X-RAY JRNL TITL 2 CRYSTALLOGRAPHIC STUDY OF THE AQUO-MET AND JRNL TITL 3 CYANO-MET DERIVATIVES OF THE LOGGERHEAD SEA TURTLE JRNL TITL 4 (CARETTA CARETTA) MYOGLOBIN AT 2.0 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 247 459 1995 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.CONTI,C.MOSER,M.RIZZI,A.MATTEVI,C.LIONETTI, REMARK 1 AUTH 2 A.CODA,P.ASCENZI,M.BRUNORI,M.BOLOGNESI REMARK 1 TITL X-RAY CRYSTAL STRUCTURE OF APLYSIA LIMACINA REMARK 1 TITL 2 MYOGLOBIN IN DIFFERENT LIGANDED STATES REMARK 1 REF J.MOL.BIOL. V. 233 498 1993 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.PETRUZZELLI,G.AURELI,E.CASALE,M.NARDINI,M.RIZZI, REMARK 1 AUTH 2 P.ASCENZI,M.COLETTA,G.DE SANCTIS,A.DESIDERI, REMARK 1 AUTH 3 A.GALTIERI,M.BOLOGNESI REMARK 1 TITL STRUCTURAL STUDIES ON THE LOGGERHEAD SEA TURTLE REMARK 1 TITL 2 (CARETTA CARETTA) MYOGLOBIN REMARK 1 REF BIOCHEM.MOL.BIOL.INT. V. 31 19 1993 REMARK 1 REFN ASTM BMBIES AT ISSN 1039-9712 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT, X-PLOR 3.1 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) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13820 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) :0.182 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 : 1139 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 63 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) : NULL ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : NULL ; 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 1LHS 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 : 02-OCT-1994 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N 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 : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13820 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 4.000 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: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 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 18.75000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.60000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.60000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.75000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.55000 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 ASP A 5 OD1 OD2 REMARK 470 ARG A 31 CD NE CZ NH1 NH2 REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 ARG A 42 NH2 REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 LYS A 47 CB CG CD CE NZ REMARK 470 ASN A 48 CB CG OD1 ND2 REMARK 470 THR A 51 OG1 CG2 REMARK 470 ILE A 52 CG1 CD1 REMARK 470 ASP A 53 CG OD1 OD2 REMARK 470 LYS A 56 CB CG CD CE NZ REMARK 470 GLU A 59 CG CD OE1 OE2 REMARK 470 LYS A 62 NZ REMARK 470 LYS A 63 CE NZ REMARK 470 GLN A 78 CD OE1 NE2 REMARK 470 GLU A 83 CD OE1 OE2 REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 LYS A 96 CE NZ REMARK 470 LYS A 98 CD CE NZ REMARK 470 LYS A 102 CD CE NZ REMARK 470 GLU A 109 CG CD OE1 OE2 REMARK 470 LYS A 113 CG CD CE NZ REMARK 470 LYS A 132 NZ REMARK 470 LYS A 133 NZ REMARK 470 ARG A 139 NH2 REMARK 470 LYS A 145 CD CE NZ REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 GLN A 152 CB CG CD OE1 NE2 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 FE HEM 155 O HOH 328 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 O GLU A 105 O HOH 312 1545 2.19 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 LEU A 21 C SER A 22 N -0.168 REMARK 500 LYS A 56 C SER A 57 N 0.118 REMARK 500 ALA A 94 C THR A 95 N 0.130 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 ASP A 5 O - C - N ANGL. DEV. =-16.6 DEGREES REMARK 500 THR A 50 CB - CA - C ANGL. DEV. = 18.4 DEGREES REMARK 500 THR A 50 N - CA - CB ANGL. DEV. =-19.8 DEGREES 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 250 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH 301 DISTANCE = 8.41 ANGSTROMS REMARK 525 HOH 312 DISTANCE = 37.98 ANGSTROMS REMARK 525 HOH 316 DISTANCE = 5.72 ANGSTROMS REMARK 525 HOH 323 DISTANCE = 5.82 ANGSTROMS DBREF 1LHS A 1 153 UNP P56208 MYG_CARCR 1 153 SEQRES 1 A 153 GLY LEU SER ASP ASP GLU TRP ASN HIS VAL LEU GLY ILE SEQRES 2 A 153 TRP ALA LYS VAL GLU PRO ASP LEU SER ALA HIS GLY GLN SEQRES 3 A 153 GLU VAL ILE ILE ARG LEU PHE GLN LEU HIS PRO GLU THR SEQRES 4 A 153 GLN GLU ARG PHE ALA LYS PHE LYS ASN LEU THR THR ILE SEQRES 5 A 153 ASP ALA LEU LYS SER SER GLU GLU VAL LYS LYS HIS GLY SEQRES 6 A 153 THR THR VAL LEU THR ALA LEU GLY ARG ILE LEU LYS GLN SEQRES 7 A 153 LYS ASN ASN HIS GLU GLN GLU LEU LYS PRO LEU ALA GLU SEQRES 8 A 153 SER HIS ALA THR LYS HIS LYS ILE PRO VAL LYS TYR LEU SEQRES 9 A 153 GLU PHE ILE CYS GLU ILE ILE VAL LYS VAL ILE ALA GLU SEQRES 10 A 153 LYS HIS PRO SER ASP PHE GLY ALA ASP SER GLN ALA ALA SEQRES 11 A 153 MET LYS LYS ALA LEU GLU LEU PHE ARG ASN ASP MET ALA SEQRES 12 A 153 SER LYS TYR LYS GLU PHE GLY PHE GLN GLY HET HEM 155 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *63(H2 O) HELIX 1 1 ASP A 4 LEU A 35 1 32 HELIX 2 2 PRO A 37 ARG A 42 1 6 HELIX 3 3 ALA A 44 PHE A 46 5 3 HELIX 4 4 ILE A 52 LYS A 56 1 5 HELIX 5 5 GLU A 59 GLN A 78 1 20 HELIX 6 6 GLU A 83 THR A 95 1 13 HELIX 7 7 VAL A 101 LYS A 118 1 18 HELIX 8 8 ALA A 125 PHE A 149 1 25 CRYST1 37.500 61.100 75.200 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 0.026667 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013298 0.00000