HEADER OXYGEN STORAGE 02-NOV-21 7SPH TITLE CRYSTAL STRUCTURE OF SPERM WHALE MYOGLOBIN VARIANT SMB13(PCAAF) IN TITLE 2 SPACE GROUP P21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER MACROCEPHALUS; SOURCE 3 ORGANISM_COMMON: SPERM WHALE, PHYSETER CATODON; SOURCE 4 ORGANISM_TAXID: 9755; SOURCE 5 GENE: MB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEME, METALLOPROTEIN, THIOETHER, MYOGLOBIN, OXYGEN STORAGE EXPDTA X-RAY DIFFRACTION AUTHOR J.P.BACIK,R.FASAN,N.ANDO REVDAT 4 16-OCT-24 7SPH 1 LINK REVDAT 3 25-OCT-23 7SPH 1 REMARK REVDAT 2 30-NOV-22 7SPH 1 JRNL REVDAT 1 01-JUN-22 7SPH 0 JRNL AUTH J.A.IANNUZZELLI,J.P.BACIK,E.J.MOORE,Z.SHEN,E.M.IRVING, JRNL AUTH 2 D.A.VARGAS,S.D.KHARE,N.ANDO,R.FASAN JRNL TITL TUNING ENZYME THERMOSTABILITY VIA COMPUTATIONALLY GUIDED JRNL TITL 2 COVALENT STAPLING AND STRUCTURAL BASIS OF ENHANCED JRNL TITL 3 STABILIZATION. JRNL REF BIOCHEMISTRY V. 61 1041 2022 JRNL REFN ISSN 0006-2960 JRNL PMID 35612958 JRNL DOI 10.1021/ACS.BIOCHEM.2C00033 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 42977 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.160 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2157 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 31.1500 - 3.2051 0.97 2998 145 0.1398 0.1511 REMARK 3 2 3.2051 - 2.5443 0.99 2950 170 0.1445 0.1689 REMARK 3 3 2.5443 - 2.2228 0.97 2891 129 0.1324 0.1715 REMARK 3 4 2.2228 - 2.0196 0.99 2923 178 0.1237 0.1525 REMARK 3 5 2.0196 - 1.8749 0.97 2880 138 0.1293 0.1532 REMARK 3 6 1.8749 - 1.7644 0.96 2872 128 0.1257 0.1564 REMARK 3 7 1.7644 - 1.6760 0.97 2882 159 0.1177 0.1582 REMARK 3 8 1.6760 - 1.6030 0.98 2880 132 0.1123 0.1492 REMARK 3 9 1.6030 - 1.5413 0.96 2826 147 0.1196 0.1692 REMARK 3 10 1.5413 - 1.4881 0.97 2808 187 0.1136 0.1465 REMARK 3 11 1.4881 - 1.4416 0.97 2860 156 0.1229 0.1329 REMARK 3 12 1.4416 - 1.4004 0.96 2827 145 0.1320 0.1897 REMARK 3 13 1.4004 - 1.3635 0.86 2530 128 0.1560 0.2093 REMARK 3 14 1.3635 - 1.3303 0.69 1996 124 0.1805 0.2045 REMARK 3 15 1.3303 - 1.3000 0.58 1697 91 0.2010 0.1966 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.35 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7SPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000258876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42991 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 31.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.60200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6M8F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 160 NL OF PROTEIN (0.6 MM) IN 20 MM REMARK 280 TRIS PH 8.4, 1 MM EDTA, WAS MIXED WITH AN EQUAL VOLUME OF REMARK 280 RESERVOIR SOLUTION, 2.2 M AMMONIUM SULFATE, 0.2 M POTASSIUM REMARK 280 FLUORIDE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 20.81400 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 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 GLU A 83 CG CD OE1 OE2 REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 LYS A 102 CG CD CE NZ REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 524 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 525 DISTANCE = 6.70 ANGSTROMS 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 201 NA 90.9 REMARK 620 3 HEM A 201 NB 92.8 88.9 REMARK 620 4 HEM A 201 NC 100.3 168.7 90.9 REMARK 620 5 HEM A 201 ND 99.5 88.6 167.5 89.3 REMARK 620 6 OXY A 202 O1 175.3 85.2 84.5 83.5 83.1 REMARK 620 N 1 2 3 4 5 DBREF 7SPH A 0 153 UNP P02185 MYG_PHYMC 1 154 SEQADV 7SPH A3U A 5 UNP P02185 GLY 6 CONFLICT SEQADV 7SPH A3U A 36 UNP P02185 HIS 37 CONFLICT SEQADV 7SPH VAL A 64 UNP P02185 HIS 65 CONFLICT SEQADV 7SPH ALA A 68 UNP P02185 VAL 69 CONFLICT SEQADV 7SPH CYS A 109 UNP P02185 GLU 110 CONFLICT SEQADV 7SPH GLU A 113 UNP P02185 HIS 114 CONFLICT SEQADV 7SPH ASN A 122 UNP P02185 ASP 123 CONFLICT SEQADV 7SPH CYS A 126 UNP P02185 ASP 127 CONFLICT SEQRES 1 A 154 MET VAL LEU SER GLU A3U GLU TRP GLN LEU VAL LEU HIS SEQRES 2 A 154 VAL TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY SEQRES 3 A 154 GLN ASP ILE LEU ILE ARG LEU PHE LYS SER A3U PRO GLU SEQRES 4 A 154 THR LEU GLU LYS PHE ASP ARG PHE LYS HIS LEU LYS THR SEQRES 5 A 154 GLU ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS VAL SEQRES 6 A 154 GLY VAL THR ALA LEU THR ALA LEU GLY ALA ILE LEU LYS SEQRES 7 A 154 LYS LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA SEQRES 8 A 154 GLN SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR SEQRES 9 A 154 LEU GLU PHE ILE SER CYS ALA ILE ILE GLU VAL LEU HIS SEQRES 10 A 154 SER ARG HIS PRO GLY ASN PHE GLY ALA CYS ALA GLN GLY SEQRES 11 A 154 ALA MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE SEQRES 12 A 154 ALA ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY HET A3U A 5 15 HET A3U A 36 15 HET HEM A 201 43 HET OXY A 202 2 HET SO4 A 203 5 HET SO4 A 204 5 HET SO4 A 205 5 HETNAM A3U 4-ACETAMIDO-L-PHENYLALANINE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE HETNAM SO4 SULFATE ION HETSYN HEM HEME FORMUL 1 A3U 2(C11 H14 N2 O3) FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 OXY O2 FORMUL 4 SO4 3(O4 S 2-) FORMUL 7 HOH *225(H2 O) HELIX 1 AA1 SER A 3 ASP A 20 1 18 HELIX 2 AA2 ASP A 20 A3U A 36 1 17 HELIX 3 AA3 PRO A 37 LYS A 47 5 11 HELIX 4 AA4 THR A 51 ALA A 57 1 7 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 GLY A 124 LEU A 149 1 26 LINK C GLU A 4 N A3U A 5 1555 1555 1.27 LINK C A3U A 5 N GLU A 6 1555 1555 1.23 LINK C2 A3U A 5 SG CYS A 126 1555 1555 2.13 LINK C SER A 35 N A3U A 36 1555 1555 1.33 LINK C A3U A 36 N PRO A 37 1555 1555 1.34 LINK C2 A3U A 36 SG CYS A 109 1555 1555 1.77 LINK NE2 HIS A 93 FE HEM A 201 1555 1555 2.12 LINK FE HEM A 201 O1 OXY A 202 1555 1555 2.26 CRYST1 49.044 41.628 50.887 90.00 112.70 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 0.020390 0.000000 0.008529 0.00000 SCALE2 0.000000 0.024022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021301 0.00000