HEADER OXIDOREDUCTASE 31-DEC-15 5HAV TITLE SPERM WHALE MYOGLOBIN MUTANT L29H F33Y F43H (F33Y CUBMB) WITH OXYGEN TITLE 2 BOUND 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PT-7 KEYWDS OXIDASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR I.D.PETRIK,Y.LU REVDAT 6 27-SEP-23 5HAV 1 REMARK REVDAT 5 25-DEC-19 5HAV 1 REMARK REVDAT 4 20-SEP-17 5HAV 1 REMARK REVDAT 3 17-FEB-16 5HAV 1 JRNL REVDAT 2 03-FEB-16 5HAV 1 JRNL REVDAT 1 13-JAN-16 5HAV 0 JRNL AUTH I.D.PETRIK,R.DAVYDOV,M.ROSS,X.ZHAO,B.HOFFMAN,Y.LU JRNL TITL SPECTROSCOPIC AND CRYSTALLOGRAPHIC EVIDENCE FOR THE ROLE OF JRNL TITL 2 A WATER-CONTAINING H-BOND NETWORK IN OXIDASE ACTIVITY OF AN JRNL TITL 3 ENGINEERED MYOGLOBIN. JRNL REF J.AM.CHEM.SOC. V. 138 1134 2016 JRNL REFN ESSN 1520-5126 JRNL PMID 26716352 JRNL DOI 10.1021/JACS.5B12004 REMARK 2 REMARK 2 RESOLUTION. 1.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX PHENIX.REFINE: 1.9_1692 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) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 72950 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 3471 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 23.8358 - 3.7035 0.99 2798 152 0.1494 0.1835 REMARK 3 2 3.7035 - 2.9413 0.99 2794 134 0.1452 0.1586 REMARK 3 3 2.9413 - 2.5700 0.99 2808 122 0.1573 0.1880 REMARK 3 4 2.5700 - 2.3353 0.99 2797 155 0.1495 0.1597 REMARK 3 5 2.3353 - 2.1680 0.99 2817 131 0.1434 0.1917 REMARK 3 6 2.1680 - 2.0402 0.99 2822 133 0.1367 0.1551 REMARK 3 7 2.0402 - 1.9381 1.00 2774 161 0.1413 0.1675 REMARK 3 8 1.9381 - 1.8538 0.99 2843 134 0.1341 0.1549 REMARK 3 9 1.8538 - 1.7824 1.00 2819 138 0.1407 0.1726 REMARK 3 10 1.7824 - 1.7210 1.00 2771 132 0.1336 0.1647 REMARK 3 11 1.7210 - 1.6672 1.00 2819 147 0.1294 0.1727 REMARK 3 12 1.6672 - 1.6195 0.99 2829 149 0.1217 0.1525 REMARK 3 13 1.6195 - 1.5769 1.00 2837 141 0.1233 0.1875 REMARK 3 14 1.5769 - 1.5384 1.00 2770 140 0.1207 0.1676 REMARK 3 15 1.5384 - 1.5035 1.00 2863 144 0.1285 0.1705 REMARK 3 16 1.5035 - 1.4715 0.99 2761 134 0.1236 0.1876 REMARK 3 17 1.4715 - 1.4420 1.00 2849 139 0.1357 0.1744 REMARK 3 18 1.4420 - 1.4148 1.00 2803 143 0.1530 0.2092 REMARK 3 19 1.4148 - 1.3896 1.00 2862 139 0.1570 0.2353 REMARK 3 20 1.3896 - 1.3660 1.00 2736 135 0.1701 0.2108 REMARK 3 21 1.3660 - 1.3440 1.00 2880 147 0.1730 0.2143 REMARK 3 22 1.3440 - 1.3233 0.99 2739 133 0.1893 0.2641 REMARK 3 23 1.3233 - 1.3038 0.96 2786 142 0.1990 0.2459 REMARK 3 24 1.3038 - 1.2855 0.92 2546 128 0.2148 0.2656 REMARK 3 25 1.2855 - 1.2681 0.82 2356 118 0.2218 0.2288 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.24 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 : 0.017 1368 REMARK 3 ANGLE : 2.097 1856 REMARK 3 CHIRALITY : 0.076 194 REMARK 3 PLANARITY : 0.011 228 REMARK 3 DIHEDRAL : 18.641 521 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 5HAV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000211478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7-7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39055 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.268 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.32900 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4FWX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION SOLUTION: 30% PEG REMARK 280 10000, 200 MM SODIUM ACETATE, 100 MM SODIUM MES PH 6.75 PROTEIN REMARK 280 SOLUTION: 1 MM PROTEIN, 20 MM TRIS SULFATE PH 8.0, SOLUTIONS REMARK 280 MIXED 1:1 AT 200UL FINAL VOLUME AND EQUILIBRATED BY SITTING DROP REMARK 280 VAPOR DIFFUSION AGAINST 30 ML OF CRYSTALLIZATION SOLUTION IN THE REMARK 280 DARK, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 19.81600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.26700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.80450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.26700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.81600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.80450 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 OE1 GLU A 38 O HOH A 302 2.00 REMARK 500 O HOH A 355 O HOH A 394 2.17 REMARK 500 OE1 GLU A 38 O HOH A 303 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 ASP A 20 71.10 -156.28 REMARK 500 LYS A 98 65.40 60.06 REMARK 500 LYS A 98 64.93 60.47 REMARK 500 PHE A 123 56.71 -147.90 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 92.7 88.4 REMARK 620 4 HEM A 201 NC 98.9 169.5 90.6 REMARK 620 5 HEM A 201 ND 96.2 87.9 170.5 91.5 REMARK 620 6 OXY A 202 O1 155.6 107.0 103.1 63.1 69.6 REMARK 620 7 OXY A 202 O2 177.5 87.7 89.6 81.9 81.4 23.5 REMARK 620 N 1 2 3 4 5 6 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 OXY A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FWX RELATED DB: PDB REMARK 900 THIS CONTAINS THE SAME PROTEIN AS 4FWX BOUND TO OXYGEN. DBREF 5HAV A 1 153 UNP P02185 MYG_PHYCD 2 154 SEQADV 5HAV HIS A 29 UNP P02185 LEU 30 ENGINEERED MUTATION SEQADV 5HAV TYR A 33 UNP P02185 PHE 34 ENGINEERED MUTATION SEQADV 5HAV HIS A 43 UNP P02185 PHE 44 ENGINEERED MUTATION 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 HIS ILE ARG LEU TYR LYS SER HIS PRO GLU THR SEQRES 4 A 153 LEU GLU LYS HIS 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 HEM A 201 43 HET OXY A 202 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 OXY O2 FORMUL 4 HOH *241(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 PRO A 37 LYS A 47 5 11 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 LEU A 149 1 26 LINK NE2 HIS A 93 FE HEM A 201 1555 1555 2.07 LINK FE HEM A 201 O1 OXY A 202 1555 1555 2.67 LINK FE HEM A 201 O2 OXY A 202 1555 1555 1.84 SITE 1 AC1 19 LYS A 42 HIS A 43 ARG A 45 HIS A 64 SITE 2 AC1 19 THR A 67 VAL A 68 LEU A 89 SER A 92 SITE 3 AC1 19 HIS A 93 HIS A 97 ILE A 99 TYR A 103 SITE 4 AC1 19 OXY A 202 HOH A 316 HOH A 335 HOH A 392 SITE 5 AC1 19 HOH A 427 HOH A 445 HOH A 462 SITE 1 AC2 5 HIS A 43 HIS A 64 VAL A 68 HEM A 201 SITE 2 AC2 5 HOH A 301 CRYST1 39.632 47.609 76.534 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 0.025232 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013066 0.00000