HEADER OXYGEN TRANSPORT 27-NOV-13 4NS2 TITLE CRYSTAL STRUCTURE OF HORSE HEART FERRIC MYOGLOBIN; D44K/D60K/E85K TITLE 2 MUTANT 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: EQUUS CABALLUS; SOURCE 3 ORGANISM_COMMON: DOMESTIC HORSE,EQUINE; SOURCE 4 ORGANISM_TAXID: 9796; SOURCE 5 GENE: MB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR I.SPAN,A.C.ROSENZWEIG REVDAT 3 20-SEP-23 4NS2 1 REMARK REVDAT 2 26-AUG-20 4NS2 1 JRNL REMARK SEQADV REVDAT 1 24-DEC-14 4NS2 0 JRNL AUTH E.N.TRANA,J.M.NOCEK,J.V.WOUDE,I.SPAN,S.M.SMITH, JRNL AUTH 2 A.C.ROSENZWEIG,B.M.HOFFMAN JRNL TITL CHARGE-DISPROPORTIONATION SYMMETRY BREAKING CREATES A JRNL TITL 2 HETERODIMERIC MYOGLOBIN COMPLEX WITH ENHANCED AFFINITY AND JRNL TITL 3 RAPID INTRACOMPLEX ELECTRON TRANSFER. JRNL REF J.AM.CHEM.SOC. V. 138 12615 2016 JRNL REFN ESSN 1520-5126 JRNL PMID 27646786 JRNL DOI 10.1021/JACS.6B07672 REMARK 2 REMARK 2 RESOLUTION. 1.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 46602 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.190 REMARK 3 FREE R VALUE TEST SET COUNT : 1954 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 28.2683 - 2.8431 1.00 3419 150 0.1801 0.2225 REMARK 3 2 2.8431 - 2.2569 1.00 3320 143 0.1720 0.1768 REMARK 3 3 2.2569 - 1.9717 1.00 3303 145 0.1531 0.1389 REMARK 3 4 1.9717 - 1.7915 0.99 3267 142 0.1499 0.1622 REMARK 3 5 1.7915 - 1.6631 0.99 3297 144 0.1459 0.1652 REMARK 3 6 1.6631 - 1.5651 0.99 3268 142 0.1417 0.1972 REMARK 3 7 1.5651 - 1.4867 0.98 3212 140 0.1371 0.1792 REMARK 3 8 1.4867 - 1.4220 0.98 3225 141 0.1493 0.1811 REMARK 3 9 1.4220 - 1.3672 0.97 3185 139 0.1659 0.1822 REMARK 3 10 1.3672 - 1.3200 0.96 3122 138 0.1818 0.2371 REMARK 3 11 1.3200 - 1.2788 0.94 3081 135 0.1960 0.1982 REMARK 3 12 1.2788 - 1.2422 0.92 3000 135 0.2113 0.2730 REMARK 3 13 1.2422 - 1.2095 0.92 3018 131 0.2380 0.2610 REMARK 3 14 1.2095 - 1.1800 0.90 2931 129 0.2583 0.2881 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) : 18.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 1282 REMARK 3 ANGLE : 1.087 1734 REMARK 3 CHIRALITY : 0.036 178 REMARK 3 PLANARITY : 0.005 213 REMARK 3 DIHEDRAL : 14.977 464 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 4NS2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083585. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 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 : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.078 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47934 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.180 REMARK 200 RESOLUTION RANGE LOW (A) : 30.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.70200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 1YMB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.3 M AMMONIUM SULFATE, 0.1 M TRIS PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, 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 15.18000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 50 O HOH A 375 1455 1.98 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 71.50 -153.87 REMARK 500 LYS A 79 -127.20 52.46 REMARK 500 HIS A 81 56.91 -111.29 REMARK 500 THR A 95 -77.08 -128.72 REMARK 500 LYS A 98 97.20 -69.28 REMARK 500 PHE A 123 54.21 -150.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 SO4 A 201 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 202 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 202 NA 90.3 REMARK 620 3 HEM A 202 NB 90.9 88.8 REMARK 620 4 HEM A 202 NC 95.2 174.2 89.5 REMARK 620 5 HEM A 202 ND 93.8 90.5 175.3 90.7 REMARK 620 6 HOH A 402 O 177.0 92.7 89.6 81.8 85.7 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 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A6N RELATED DB: PDB REMARK 900 DEOXY-MYOGLOBIN, ATOMIC RESOLUTION REMARK 900 RELATED ID: 1YMB RELATED DB: PDB REMARK 900 HIGH RESOLUTION STUDY OF THE THREE-DIMENSIONAL STRUCTURE OF HORSE REMARK 900 HEART METMYOGLOBIN REMARK 900 RELATED ID: 2IN4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYOGLOBIN WITH CHARGE NEUTRALIZED HEME, ZNDMB- REMARK 900 DME REMARK 900 RELATED ID: 3RJN RELATED DB: PDB REMARK 900 HORSE HEART MYOGLOBIN: D44K/D60K MUTANT WITH ZINC (II) - REMARK 900 DEUTEROPORPHYRIN DIMETHYL ESTER REMARK 900 RELATED ID: 3RJ6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HORSE HEART FERRIC MYOGLOBIN; K45E/K63E/K96E REMARK 900 MUTANT DBREF 4NS2 A 0 153 UNP P68082 MYG_HORSE 1 154 SEQADV 4NS2 LYS A 44 UNP P68082 ASP 45 ENGINEERED MUTATION SEQADV 4NS2 LYS A 60 UNP P68082 ASP 61 ENGINEERED MUTATION SEQADV 4NS2 LYS A 85 UNP P68082 GLU 86 ENGINEERED MUTATION SEQRES 1 A 154 MET GLY LEU SER ASP GLY GLU TRP GLN GLN VAL LEU ASN SEQRES 2 A 154 VAL TRP GLY LYS VAL GLU ALA ASP ILE ALA GLY HIS GLY SEQRES 3 A 154 GLN GLU VAL LEU ILE ARG LEU PHE THR GLY HIS PRO GLU SEQRES 4 A 154 THR LEU GLU LYS PHE LYS LYS PHE LYS HIS LEU LYS THR SEQRES 5 A 154 GLU ALA GLU MET LYS ALA SER GLU LYS LEU LYS LYS HIS SEQRES 6 A 154 GLY THR VAL VAL LEU THR ALA LEU GLY GLY ILE LEU LYS SEQRES 7 A 154 LYS LYS GLY HIS HIS GLU ALA LYS 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 ASP ALA ILE ILE HIS VAL LEU HIS SEQRES 10 A 154 SER LYS HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY SEQRES 11 A 154 ALA MET THR LYS ALA LEU GLU LEU PHE ARG ASN ASP ILE SEQRES 12 A 154 ALA ALA LYS TYR LYS GLU LEU GLY PHE GLN GLY HET SO4 A 201 5 HET HEM A 202 43 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 SO4 O4 S 2- FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *113(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 ALA A 57 1 7 HELIX 5 5 SER A 58 LYS A 78 1 21 HELIX 6 6 HIS A 82 HIS A 93 1 12 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 202 1555 1555 2.13 LINK FE HEM A 202 O HOH A 402 1555 1555 2.19 SITE 1 AC1 17 THR A 39 LYS A 42 PHE A 43 LYS A 45 SITE 2 AC1 17 HIS A 64 VAL 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 HOH A 330 HOH A 344 SITE 5 AC1 17 HOH A 402 CRYST1 42.820 30.360 56.990 90.00 97.36 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 0.023354 0.000000 0.003017 0.00000 SCALE2 0.000000 0.032938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017693 0.00000