HEADER OXYGEN STORAGE 22-JUN-10 3NML TITLE SPERM WHALE MYOGLOBIN MUTANT H64W CARBONMONOXY-FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PHAGE RESISTANT TB1; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PUC19 KEYWDS MYOGLOBIN, LIGAND MIGRATION PATHWAYS, OXYGEN STORAGE EXPDTA X-RAY DIFFRACTION AUTHOR I.BIRUKOU,J.SOMAN,J.S.OLSON REVDAT 5 06-SEP-23 3NML 1 REMARK SEQADV REVDAT 4 17-JUL-19 3NML 1 REMARK REVDAT 3 13-APR-11 3NML 1 JRNL REVDAT 2 19-JAN-11 3NML 1 JRNL REVDAT 1 14-JUL-10 3NML 0 JRNL AUTH I.BIRUKOU,J.SOMAN,J.S.OLSON JRNL TITL BLOCKING THE GATE TO LIGAND ENTRY IN HUMAN HEMOGLOBIN. JRNL REF J.BIOL.CHEM. V. 286 10515 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21193395 JRNL DOI 10.1074/JBC.M110.176271 REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.1_357 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 19099 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1909 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 22.7135 - 4.0418 1.00 1349 151 0.1730 0.1692 REMARK 3 2 4.0418 - 3.2110 1.00 1269 141 0.1416 0.1758 REMARK 3 3 3.2110 - 2.8059 1.00 1263 140 0.1656 0.2166 REMARK 3 4 2.8059 - 2.5497 1.00 1249 139 0.1519 0.1823 REMARK 3 5 2.5497 - 2.3672 1.00 1233 136 0.1268 0.1454 REMARK 3 6 2.3672 - 2.2278 1.00 1245 138 0.1220 0.1603 REMARK 3 7 2.2278 - 2.1163 1.00 1223 136 0.1291 0.1610 REMARK 3 8 2.1163 - 2.0242 0.99 1225 135 0.1403 0.1815 REMARK 3 9 2.0242 - 1.9463 1.00 1220 136 0.1476 0.2103 REMARK 3 10 1.9463 - 1.8792 0.98 1201 134 0.1527 0.1956 REMARK 3 11 1.8792 - 1.8205 0.98 1200 133 0.1497 0.1842 REMARK 3 12 1.8205 - 1.7684 0.99 1213 135 0.1391 0.1871 REMARK 3 13 1.7684 - 1.7219 0.97 1194 133 0.1505 0.2003 REMARK 3 14 1.7219 - 1.6800 0.92 1106 122 0.1550 0.2121 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 : 0.42 REMARK 3 B_SOL : 40.31 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.25070 REMARK 3 B22 (A**2) : -0.90860 REMARK 3 B33 (A**2) : -0.34200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.019 1381 REMARK 3 ANGLE : 1.242 1883 REMARK 3 CHIRALITY : 0.064 191 REMARK 3 PLANARITY : 0.005 234 REMARK 3 DIHEDRAL : 13.890 508 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 3NML COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000060016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19145 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 41.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.710 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.15900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2MBW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION (20MG/ML PROTEIN IN REMARK 280 0.02M TRIS-HCL PH9.0) MIXED WITH MOTHER LIQUOR (3.2M AMMONIUM REMARK 280 SULPHATE, 0.05M TRIS-HCL, PH9.0) FOR FINAL CONCENTRATIONS OF REMARK 280 2.5M AMMONIUM SULPHATE, BATCH METHOD, TEMPERATURE 293K 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 19.46500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.75000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.48000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.75000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.46500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.48000 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 HE2 HIS A 93 FE HEM A 154 1.25 REMARK 500 HE2 HIS A 24 HE2 HIS A 119 1.29 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 72.35 -152.49 REMARK 500 PHE A 123 55.47 -142.27 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 91.4 REMARK 620 3 HEM A 154 NB 90.4 88.9 REMARK 620 4 HEM A 154 NC 92.2 176.4 90.6 REMARK 620 5 HEM A 154 ND 92.7 88.9 176.3 91.3 REMARK 620 6 CMO A 155 C 174.4 87.6 95.1 88.9 81.8 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 HEM A 154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CMO A 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 158 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NMM RELATED DB: PDB REMARK 900 HUMAN HEMOGLOBIN A MUTANT ALPHA H58W DEOXY-FORM DBREF 3NML A 0 153 UNP P02185 MYG_PHYCA 1 154 SEQADV 3NML TRP A 64 UNP P02185 HIS 65 ENGINEERED MUTATION SEQADV 3NML ASN A 122 UNP P02185 ASP 123 VARIANT 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 TRP 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 ASN 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 154 73 HET CMO A 155 2 HET SO4 A 156 5 HET SO4 A 157 5 HET SO4 A 158 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 3(O4 S 2-) FORMUL 7 HOH *233(H2 O) HELIX 1 1 SER A 3 GLU A 18 1 16 HELIX 2 2 ASP A 20 HIS A 36 1 17 HELIX 3 3 PRO A 37 PHE A 43 5 7 HELIX 4 4 THR A 51 SER A 58 1 8 HELIX 5 5 SER A 58 LYS A 78 1 21 HELIX 6 6 HIS A 82 LYS A 96 1 15 HELIX 7 7 PRO A 100 HIS A 119 1 20 HELIX 8 8 PRO A 120 PHE A 123 5 4 HELIX 9 9 GLY A 124 LEU A 149 1 26 LINK NE2 HIS A 93 FE HEM A 154 1555 1555 2.10 LINK FE HEM A 154 C CMO A 155 1555 1555 1.54 SITE 1 AC1 21 THR A 39 LYS A 42 PHE A 43 ARG A 45 SITE 2 AC1 21 LYS A 62 TRP A 64 THR A 67 VAL A 68 SITE 3 AC1 21 LEU A 89 SER A 92 HIS A 93 HIS A 97 SITE 4 AC1 21 ILE A 99 TYR A 103 LEU A 104 CMO A 155 SITE 5 AC1 21 HOH A 237 HOH A 238 HOH A 239 HOH A 298 SITE 6 AC1 21 HOH A 322 SITE 1 AC2 4 PHE A 43 VAL A 68 HIS A 93 HEM A 154 SITE 1 AC3 7 MET A 0 LYS A 42 GLU A 136 LYS A 140 SITE 2 AC3 7 HOH A 222 HOH A 323 HOH A 366 SITE 1 AC4 5 LYS A 63 HIS A 113 HOH A 168 HOH A 285 SITE 2 AC4 5 HOH A 354 SITE 1 AC5 4 LYS A 34 THR A 51 GLU A 52 HOH A 369 CRYST1 38.930 46.960 89.500 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 0.025687 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021295 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011173 0.00000