HEADER OXYGEN TRANSPORT 06-NOV-18 6N03 TITLE CO-BOUND SPERM WHALE MYOGLOBIN, ROOM TEMPERATURE STRUCTURE, LAST 2 TITLE 2 DEGREES OF 5 DEGREE TOTAL OSCILLATION AND 160 KGY DOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN, CO-BOUND; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; SOURCE 3 ORGANISM_COMMON: SPERM WHALE; SOURCE 4 ORGANISM_TAXID: 9755; SOURCE 5 GENE: MB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXYGEN TRANSPORTER, MYOGLOBIN, TRANSPORT PROTEIN, OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.D.FINKE,J.L.WIERMAN,O.PARE-LABROSSE,A.SARRACHINI,J.BESAW,P.MEHRABI, AUTHOR 2 S.M.GRUNER,R.J.D.MILLER REVDAT 3 11-OCT-23 6N03 1 REMARK REVDAT 2 27-NOV-19 6N03 1 REMARK REVDAT 1 27-MAR-19 6N03 0 JRNL AUTH J.L.WIERMAN,O.PARE-LABROSSE,A.SARRACINI,J.E.BESAW,M.J.COOK, JRNL AUTH 2 S.OGHBAEY,H.DAOUD,P.MEHRABI,I.KRIKSUNOV,A.KUO,D.J.SCHULLER, JRNL AUTH 3 S.SMITH,O.P.ERNST,D.M.E.SZEBENYI,S.M.GRUNER,R.J.D.MILLER, JRNL AUTH 4 A.D.FINKE JRNL TITL FIXED-TARGET SERIAL OSCILLATION CRYSTALLOGRAPHY AT ROOM JRNL TITL 2 TEMPERATURE. JRNL REF IUCRJ V. 6 305 2019 JRNL REFN ESSN 2052-2525 JRNL PMID 30867928 JRNL DOI 10.1107/S2052252519001453 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.860 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 15779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 774 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 40.1600 - 3.8100 1.00 2521 130 0.1629 0.2407 REMARK 3 2 3.8100 - 3.0300 1.00 2514 129 0.1763 0.2699 REMARK 3 3 3.0300 - 2.6500 1.00 2520 126 0.2175 0.3549 REMARK 3 4 2.6500 - 2.4000 0.99 2506 128 0.2724 0.3690 REMARK 3 5 2.4000 - 2.2300 0.99 2493 131 0.3062 0.3166 REMARK 3 6 2.2300 - 2.1000 0.98 2451 130 0.3590 0.4098 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.389 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.836 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.03 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 1320 REMARK 3 ANGLE : 1.017 1788 REMARK 3 CHIRALITY : 0.055 184 REMARK 3 PLANARITY : 0.004 221 REMARK 3 DIHEDRAL : 5.443 1070 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 6N03 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000237946. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : G3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.216 REMARK 200 MONOCHROMATOR : W/B4C MULTILAYER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 1M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8687 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 17.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 16.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.040 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: 1VXA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CO-SWMB CRYSTALS WERE HOMOGENIZED IN REMARK 280 10 MM TRIS-HCL PH 9.0 AND 3.2 M AMMONIUM SULFATE AND WASHED TWO REMARK 280 TO THREE TIMES WITH THE SAME CO-SATURATED SOLUTION., BATCH MODE, REMARK 280 TEMPERATURE 295K 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 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 18.51500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.45500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.45500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.51500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.95000 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 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 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 DISTANCE REMARK 500 NZ LYS A 42 O HOH A 301 2.07 REMARK 500 FE HEM A 201 C CMO A 202 2.14 REMARK 500 NZ LYS A 96 O HOH A 302 2.19 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 GLN A 152 151.00 69.73 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 201 NA 91.6 REMARK 620 3 HEM A 201 NB 90.9 93.9 REMARK 620 4 HEM A 201 NC 88.6 178.8 84.8 REMARK 620 5 HEM A 201 ND 90.0 89.3 176.6 91.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CMO 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6MV0 RELATED DB: PDB REMARK 900 SAME DATASET BUT FULL 5 DEGREES USED REMARK 900 RELATED ID: 6N02 RELATED DB: PDB REMARK 900 SAME DATASET BUT FIRST TWO DEGREES USED DBREF 6N03 A 0 153 UNP P02185 MYG_PHYCD 1 154 SEQRES 1 A 154 MET VAL LEU SER GLU GLY 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 HIS 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 HIS SEQRES 6 A 154 GLY VAL THR VAL 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 GLU ALA ILE ILE HIS VAL LEU HIS SEQRES 10 A 154 SER ARG HIS PRO GLY ASP PHE GLY ALA ASP 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 HEM A 201 43 HET CMO A 202 2 HET SO4 A 203 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CMO CARBON MONOXIDE HETNAM SO4 SULFATE ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CMO C O FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *16(H2 O) HELIX 1 AA1 SER A 3 ALA A 19 1 17 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 GLY A 124 LEU A 149 1 26 LINK NE2 HIS A 93 FE HEM A 201 1555 1555 1.98 SITE 1 AC1 17 THR A 39 LYS A 42 PHE A 43 ARG A 45 SITE 2 AC1 17 HIS A 64 THR A 67 VAL A 68 ALA A 71 SITE 3 AC1 17 LEU A 89 SER A 92 HIS A 93 HIS A 97 SITE 4 AC1 17 ILE A 99 TYR A 103 LEU A 104 CMO A 202 SITE 5 AC1 17 HOH A 305 SITE 1 AC2 3 PHE A 43 HIS A 64 HEM A 201 SITE 1 AC3 5 ALA A 57 SER A 58 GLU A 59 ASP A 60 SITE 2 AC3 5 LYS A 87 CRYST1 37.030 45.900 82.910 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 0.027005 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012061 0.00000