HEADER OXYGEN TRANSPORT 07-SEP-21 7VDN TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF SPERM WHALE MYOGLOBIN IN THE TITLE 2 CARBONMONOXY FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-152 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; SOURCE 3 ORGANISM_COMMON: SPERM WHALE; SOURCE 4 ORGANISM_TAXID: 9755 KEYWDS MYOGLOBIN, BLOOD, HEME BINDING, METAL ION BINDING, OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR N.SHIBAYAMA,A.SATO-TOMITA,N.ISHIMOTO,S.Y.PARK REVDAT 3 29-NOV-23 7VDN 1 REMARK REVDAT 2 05-APR-23 7VDN 1 JRNL REVDAT 1 14-SEP-22 7VDN 0 JRNL AUTH A.SATO-TOMITA,A.K.R.ANG,K.KIMURA,R.MARUMI,N.HAPPO, JRNL AUTH 2 T.MATSUSHITA,S.Y.PARK,N.SHIBAYAMA,Y.C.SASAKI,K.HAYASHI JRNL TITL X-RAY FLUORESCENCE HOLOGRAPHY OF BIOLOGICAL METAL SITES: JRNL TITL 2 APPLICATION TO MYOGLOBIN. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 635 277 2022 JRNL REFN ESSN 1090-2104 JRNL PMID 36308907 JRNL DOI 10.1016/J.BBRC.2022.10.003 REMARK 2 REMARK 2 RESOLUTION. 0.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 85826 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4297 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 20.0200 - 2.8900 1.00 2866 133 0.1748 0.1971 REMARK 3 2 2.8900 - 2.2900 1.00 2762 161 0.1819 0.2082 REMARK 3 3 2.2900 - 2.0000 1.00 2773 137 0.1613 0.1976 REMARK 3 4 2.0000 - 1.8200 1.00 2778 144 0.1590 0.1943 REMARK 3 5 1.8200 - 1.6900 1.00 2733 165 0.1497 0.1757 REMARK 3 6 1.6900 - 1.5900 1.00 2759 142 0.1362 0.1661 REMARK 3 7 1.5900 - 1.5100 1.00 2744 146 0.1272 0.1475 REMARK 3 8 1.5100 - 1.4400 1.00 2691 169 0.1211 0.1599 REMARK 3 9 1.4400 - 1.3900 1.00 2733 143 0.1292 0.1597 REMARK 3 10 1.3900 - 1.3400 1.00 2778 124 0.1262 0.1411 REMARK 3 11 1.3400 - 1.3000 1.00 2728 159 0.1270 0.1577 REMARK 3 12 1.3000 - 1.2600 1.00 2735 136 0.1240 0.1665 REMARK 3 13 1.2600 - 1.2300 1.00 2695 157 0.1311 0.1447 REMARK 3 14 1.2300 - 1.2000 1.00 2746 146 0.1513 0.1870 REMARK 3 15 1.2000 - 1.1700 1.00 2740 165 0.1771 0.2040 REMARK 3 16 1.1700 - 1.1500 1.00 2657 152 0.2387 0.2562 REMARK 3 17 1.1500 - 1.1200 1.00 2758 128 0.3149 0.3049 REMARK 3 18 1.1200 - 1.1000 1.00 2730 130 0.3859 0.3606 REMARK 3 19 1.1000 - 1.0800 1.00 2713 152 0.3867 0.3660 REMARK 3 20 1.0800 - 1.0600 0.99 2716 141 0.3984 0.4265 REMARK 3 21 1.0600 - 1.0500 0.99 2709 130 0.3943 0.4291 REMARK 3 22 1.0500 - 1.0300 0.99 2740 139 0.4127 0.4137 REMARK 3 23 1.0300 - 1.0200 1.00 2699 123 0.4193 0.4012 REMARK 3 24 1.0200 - 1.0000 1.00 2721 126 0.4136 0.3455 REMARK 3 25 1.0000 - 0.9900 0.99 2735 139 0.4031 0.4074 REMARK 3 26 0.9900 - 0.9800 0.99 2713 126 0.3974 0.4076 REMARK 3 27 0.9800 - 0.9600 0.99 2657 150 0.3990 0.4171 REMARK 3 28 0.9600 - 0.9500 0.96 2587 138 0.4033 0.4099 REMARK 3 29 0.9500 - 0.9400 0.94 2553 149 0.4254 0.4532 REMARK 3 30 0.9400 - 0.9300 0.96 2580 147 0.5589 0.5307 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.184 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.418 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.22 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1295 REMARK 3 ANGLE : 1.084 1756 REMARK 3 CHIRALITY : 0.078 181 REMARK 3 PLANARITY : 0.008 214 REMARK 3 DIHEDRAL : 15.598 465 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7VDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300024421. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54056 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 86393 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.930 REMARK 200 RESOLUTION RANGE LOW (A) : 20.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.91400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1VXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8 M AMMONIUM SULFATE, 50 MM K2HPO4, REMARK 280 50 MM NAH2PO4, 10% GLYCEROL, 2 MG/ML SODIUM DITHIONITE, BATCH REMARK 280 MODE, TEMPERATURE 293K 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 15.35100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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: 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 67.69 -154.96 REMARK 500 PHE A 123 44.53 -143.33 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 204 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 204 NA 89.8 REMARK 620 3 HEM A 204 NB 89.7 90.2 REMARK 620 4 HEM A 204 NC 91.7 178.5 89.6 REMARK 620 5 HEM A 204 ND 91.0 89.1 179.0 91.1 REMARK 620 6 CMO A 205 C 174.7 95.4 91.2 83.1 88.2 REMARK 620 N 1 2 3 4 5 DBREF 7VDN A 1 151 UNP P02185 MYG_PHYCD 2 152 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 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET HEM A 204 43 HET CMO A 205 2 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CMO CARBON MONOXIDE HETSYN HEM HEME FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HEM C34 H32 FE N4 O4 FORMUL 6 CMO C O FORMUL 7 HOH *130(H2 O) HELIX 1 AA1 SER A 3 GLU A 18 1 16 HELIX 2 AA2 ASP A 20 HIS A 36 1 17 HELIX 3 AA3 HIS A 36 GLU A 41 1 6 HELIX 4 AA4 THR A 51 SER A 58 1 8 HELIX 5 AA5 SER A 58 LYS A 78 1 21 HELIX 6 AA6 HIS A 82 LYS A 96 1 15 HELIX 7 AA7 PRO A 100 HIS A 119 1 20 HELIX 8 AA8 PRO A 120 PHE A 123 5 4 HELIX 9 AA9 GLY A 124 GLY A 150 1 27 LINK NE2 HIS A 93 FE HEM A 204 1555 1555 2.10 LINK FE HEM A 204 C CMO A 205 1555 1555 1.72 CRYST1 34.403 30.702 63.804 90.00 105.57 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 0.029067 0.000000 0.008097 0.00000 SCALE2 0.000000 0.032571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016270 0.00000