HEADER HEME PROTEIN 26-FEB-98 1A6K TITLE AQUOMET-MYOGLOBIN, ATOMIC RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; SOURCE 3 ORGANISM_COMMON: SPERM WHALE; SOURCE 4 ORGANISM_TAXID: 9755 KEYWDS HEME PROTEIN, MODEL COMPOUNDS, OXYGEN STORAGE, LIGAND BINDING KEYWDS 2 GEOMETRY, CONFORMATIONAL SUBSTATES EXPDTA X-RAY DIFFRACTION AUTHOR J.VOJTECHOVSKY,J.BERENDZEN,K.CHU,I.SCHLICHTING,R.M.SWEET REVDAT 5 22-MAY-24 1A6K 1 REMARK REVDAT 4 02-AUG-23 1A6K 1 REMARK LINK REVDAT 3 24-FEB-09 1A6K 1 VERSN REVDAT 2 14-JUN-05 1A6K 1 AUTHOR JRNL REVDAT 1 06-APR-99 1A6K 0 JRNL AUTH J.VOJTECHOVSKY,K.CHU,J.BERENDZEN,R.M.SWEET,I.SCHLICHTING JRNL TITL CRYSTAL STRUCTURES OF MYOGLOBIN-LIGAND COMPLEXES AT JRNL TITL 2 NEAR-ATOMIC RESOLUTION. JRNL REF BIOPHYS.J. V. 77 2153 1999 JRNL REFN ISSN 0006-3495 JRNL PMID 10512835 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.132 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.131 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2541 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 51286 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.125 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.124 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2330 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 46498 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1204 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 185 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1420.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1263.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 26 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 14244 REMARK 3 NUMBER OF RESTRAINTS : 18493 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.034 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.023 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.098 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.127 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.007 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.071 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: HEME - PARAMETERS BASED ON CSD REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 NO GEOMETRIC RESTRAINTS APPLIED TO IRON AND THE PLANAR ATOMS OF REMARK 3 THE HEME. REMARK 3 REMARK 3 BAYESIAN DIFFERENCE REFINEMENT WAS USED AT THE FINAL STEP. REMARK 3 SEE TERWILLIGER AND BERENDZEN, ACTA CRYST. D52:1004-1011. REMARK 3 (1996). REMARK 3 REMARK 3 THE SOLVENT MOLECULES 81, 129, 130, 139 AND 151 CAN BE REMARK 3 MODELED ONLY FOR ONE ALTERNATIVE PROTEIN CONFORMATION. REMARK 3 REMARK 3 SULFATE NEAR DISTAL HISTIDINE MODELED AS A DISORDERED REMARK 3 MOLECULE. REMARK 4 REMARK 4 1A6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170455. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-97 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51794 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 25.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29500 REMARK 200 FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1MBC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -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 15.36500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 64 CE1 HIS A 64 NE2 -0.067 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN A 26 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG A 31 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 44 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 TYR A 103 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 118 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASP A 126 CB - CG - OD1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 126 CB - CG - OD1 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG A 139 NH1 - CZ - NH2 ANGL. DEV. = -7.4 DEGREES REMARK 500 ARG A 139 NE - CZ - NH2 ANGL. DEV. = 5.9 DEGREES REMARK 500 TYR A 146 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR A 146 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 TYR A 146 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 TYR A 151 CD1 - CE1 - CZ ANGL. DEV. = -5.8 DEGREES REMARK 500 TYR A 151 CZ - CE2 - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 20 66.14 -153.63 REMARK 500 LYS A 98 62.36 60.45 REMARK 500 PHE A 123 47.37 -143.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 154 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 154 NA 93.7 REMARK 620 3 HEM A 154 NB 93.7 88.4 REMARK 620 4 HEM A 154 NC 92.3 173.7 89.2 REMARK 620 5 HEM A 154 ND 92.4 91.1 174.0 90.7 REMARK 620 6 HOH A1001 O 175.5 90.1 89.0 84.1 85.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1188 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 154 DBREF 1A6K A 1 151 UNP P02185 MYG_PHYCA 1 151 SEQRES 1 A 151 VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HIS VAL SEQRES 2 A 151 TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY GLN SEQRES 3 A 151 ASP ILE LEU ILE ARG LEU PHE LYS SER HIS PRO GLU THR SEQRES 4 A 151 LEU GLU LYS PHE ASP ARG PHE LYS HIS LEU LYS THR GLU SEQRES 5 A 151 ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS GLY SEQRES 6 A 151 VAL THR VAL LEU THR ALA LEU GLY ALA ILE LEU LYS LYS SEQRES 7 A 151 LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA GLN SEQRES 8 A 151 SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR LEU SEQRES 9 A 151 GLU PHE ILE SER GLU ALA ILE ILE HIS VAL LEU HIS SER SEQRES 10 A 151 ARG HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 151 MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE ALA SEQRES 12 A 151 ALA LYS TYR LYS GLU LEU GLY TYR HET SO4 A 155 5 HET SO4 A 156 5 HET SO4 A1188 10 HET HEM A 154 43 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HEM C34 H32 FE N4 O4 FORMUL 6 HOH *185(H2 O) HELIX 1 1 GLU A 4 SER A 35 1 32 HELIX 2 2 PRO A 37 LYS A 42 1 6 HELIX 3 3 GLU A 52 LYS A 56 1 5 HELIX 4 4 GLU A 59 LYS A 78 1 20 HELIX 5 5 GLU A 83 THR A 95 1 13 HELIX 6 6 ILE A 101 ARG A 118 1 18 HELIX 7 7 PRO A 120 ASP A 122 5 3 HELIX 8 8 ALA A 125 LEU A 149 1 25 LINK NE2 HIS A 93 FE HEM A 154 1555 1555 2.14 LINK FE HEM A 154 O HOH A1001 1555 1555 2.13 SITE 1 AC1 8 ALA A 57 SER A 58 GLU A 59 ASP A 60 SITE 2 AC1 8 HOH A1007 HOH A1026 HOH A1038 HOH A1086 SITE 1 AC2 5 GLN A 26 LYS A 62 HOH A1043 HOH A1045 SITE 2 AC2 5 HOH A1063 SITE 1 AC3 6 ARG A 45 HIS A 64 THR A 67 HIS A 116 SITE 2 AC3 6 HOH A1088 HOH A1123 SITE 1 AC4 23 THR A 39 LYS A 42 PHE A 43 ARG A 45 SITE 2 AC4 23 HIS A 64 THR A 67 VAL A 68 LEU A 89 SITE 3 AC4 23 SER A 92 HIS A 93 HIS A 97 ILE A 99 SITE 4 AC4 23 TYR A 103 LEU A 104 PHE A 138 HOH A1001 SITE 5 AC4 23 HOH A1024 HOH A1033 HOH A1059 HOH A1088 SITE 6 AC4 23 HOH A1092 HOH A1118 HOH A1149 CRYST1 63.900 30.730 34.360 90.00 105.70 90.00 P 1 21 1 2 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 0.015649 0.000000 0.004399 0.00000 SCALE2 0.000000 0.032541 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030231 0.00000