HEADER OXYGEN STORAGE 05-NOV-98 1BZ6 TITLE ATOMIC RESOLUTION CRYSTAL STRUCTURE AQUOMET-MYOGLOBIN FROM SPERM WHALE TITLE 2 AT ROOM TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (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; SOURCE 5 TISSUE: MUSCLE KEYWDS OXYGEN TRANSPORT, RESPIRATORY PROTEIN, HEME, ATOMIC RESOLUTION, KEYWDS 2 OXYGEN STORAGE EXPDTA X-RAY DIFFRACTION AUTHOR A.N.POPOV,G.S.KACHALOVA,H.D.BARTUNIK REVDAT 6 09-AUG-23 1BZ6 1 REMARK LINK REVDAT 5 04-OCT-17 1BZ6 1 REMARK REVDAT 4 24-FEB-09 1BZ6 1 VERSN REVDAT 3 01-APR-03 1BZ6 1 JRNL REVDAT 2 10-MAY-99 1BZ6 3 JRNL REMARK LINK ANISOU REVDAT 1 10-MAY-99 1BZ6 0 JRNL AUTH G.S.KACHALOVA,A.N.POPOV,H.D.BARTUNIK JRNL TITL A STERIC MECHANISM FOR INHIBITION OF CO BINDING TO HEME JRNL TITL 2 PROTEINS. JRNL REF SCIENCE V. 284 473 1999 JRNL REFN ISSN 0036-8075 JRNL PMID 10205052 JRNL DOI 10.1126/SCIENCE.284.5413.473 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.091 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) : 41485 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.088 REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 39382 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1217 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1436.8 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1034.6 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 81 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 14814 REMARK 3 NUMBER OF RESTRAINTS : 20313 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.014 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.074 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.107 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.020 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.012 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.048 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.104 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: HEME - PARAMETERS BASED ON CSD REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NO GEOMETRIC RESTRAINTS APPLIED TO IRON REMARK 3 ATOM AND HEME PLANARITY REMARK 4 REMARK 4 1BZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000000033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-97 REMARK 200 TEMPERATURE (KELVIN) : 287.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41547 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.28200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4MBN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM REMARK 280 SULPHATE, 0.1 M POTASSIUM PHOSPHATE, PH 6.0 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 15.46000 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 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 ASP A 20 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 31 NH1 - CZ - NH2 ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 31 NE - CZ - NH1 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG A 45 N - CA - CB ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 GLU A 83 OE1 - CD - OE2 ANGL. DEV. = -8.4 DEGREES REMARK 500 PHE A 123 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 ARG A 139 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 TYR A 146 CB - CG - CD1 ANGL. DEV. = 5.4 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 70.23 -154.63 REMARK 500 HIS A 81 59.45 -93.80 REMARK 500 PHE A 123 54.38 -109.01 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 90.6 REMARK 620 3 HEM A 154 NB 92.1 89.7 REMARK 620 4 HEM A 154 NC 92.8 176.5 89.2 REMARK 620 5 HEM A 154 ND 92.2 90.4 175.7 90.4 REMARK 620 6 HOH A 389 O 177.5 91.1 89.7 85.5 86.0 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 154 DBREF 1BZ6 A 1 153 UNP P02185 MYG_PHYCA 1 153 SEQRES 1 A 153 VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HIS VAL SEQRES 2 A 153 TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY GLN SEQRES 3 A 153 ASP ILE LEU ILE ARG LEU PHE LYS SER HIS PRO GLU THR SEQRES 4 A 153 LEU GLU LYS PHE ASP ARG PHE LYS HIS LEU LYS THR GLU SEQRES 5 A 153 ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS GLY SEQRES 6 A 153 VAL THR VAL LEU THR ALA LEU GLY ALA ILE LEU LYS LYS SEQRES 7 A 153 LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA GLN SEQRES 8 A 153 SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR LEU SEQRES 9 A 153 GLU PHE ILE SER GLU ALA ILE ILE HIS VAL LEU HIS SER SEQRES 10 A 153 ARG HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 153 MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE ALA SEQRES 12 A 153 ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 10 HET SO4 A 204 5 HET HEM A 154 43 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 HEM C34 H32 FE N4 O4 FORMUL 7 HOH *223(H2 O) HELIX 1 A SER A 3 GLU A 18 1 16 HELIX 2 B ASP A 20 SER A 35 1 16 HELIX 3 C HIS A 36 LYS A 42 5 7 HELIX 4 D THR A 51 ALA A 57 1 7 HELIX 5 E SER A 58 LYS A 77 1 20 HELIX 6 F LEU A 86 THR A 95 1 10 HELIX 7 G PRO A 100 ARG A 118 1 19 HELIX 8 H GLY A 124 LEU A 149 1 26 LINK NE2 HIS A 93 FE HEM A 154 1555 1555 2.16 LINK FE HEM A 154 O HOH A 389 1555 1555 2.17 SITE 1 AC1 7 SER A 58 GLU A 59 ASP A 60 HOH A 368 SITE 2 AC1 7 HOH A 376 HOH A 401 HOH A 479 SITE 1 AC2 4 PRO A 120 GLY A 121 ASP A 122 HOH A 343 SITE 1 AC3 8 ARG A 45 LYS A 63 HIS A 64 THR A 67 SITE 2 AC3 8 HIS A 116 HOH A 348 HOH A 354 HOH A 355 SITE 1 AC4 7 ARG A 31 SER A 35 LYS A 96 GLU A 109 SITE 2 AC4 7 HOH A 301 HOH A 315 HOH A 430 SITE 1 AC5 20 LYS A 42 PHE A 43 ARG A 45 HIS A 64 SITE 2 AC5 20 THR A 67 VAL A 68 LEU A 89 SER A 92 SITE 3 AC5 20 HIS A 93 HIS A 97 ILE A 99 TYR A 103 SITE 4 AC5 20 HOH A 305 HOH A 355 HOH A 378 HOH A 384 SITE 5 AC5 20 HOH A 389 HOH A 406 HOH A 440 HOH A 480 CRYST1 34.830 30.920 64.570 90.00 105.50 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 0.028711 0.000000 0.007962 0.00000 SCALE2 0.000000 0.032342 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016072 0.00000