HEADER OXIDOREDUCTASE 18-MAY-16 5K1G TITLE CRYSTAL STRUCTURE OF REDUCED PRX3 FROM VIBRIO VULNIFICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1-CYS PEROXIREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS MO6-24/O; SOURCE 3 ORGANISM_TAXID: 914127; SOURCE 4 STRAIN: MO6-24/O; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 1-CYS PRX, VIBRIO VULNIFICUS, HYDROGEN PEROXIDE, NITRIC OXIDE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.AHN,N.-C.HA REVDAT 3 08-NOV-23 5K1G 1 REMARK REVDAT 2 13-MAR-19 5K1G 1 JRNL REVDAT 1 24-MAY-17 5K1G 0 JRNL AUTH J.AHN,K.K.JANG,I.JO,H.NURHASNI,J.G.LIM,J.W.YOO,S.H.CHOI, JRNL AUTH 2 N.C.HA JRNL TITL CRYSTAL STRUCTURE OF PEROXIREDOXIN 3 FROMVIBRIO JRNL TITL 2 VULNIFICUSAND ITS IMPLICATIONS FOR SCAVENGING PEROXIDES AND JRNL TITL 3 NITRIC OXIDE. JRNL REF IUCRJ V. 5 82 2018 JRNL REFN ESSN 2052-2525 JRNL PMID 29354274 JRNL DOI 10.1107/S205225251701750X REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 14790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1471 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 31.9916 - 4.2199 0.98 1352 152 0.1717 0.2036 REMARK 3 2 4.2199 - 3.3506 1.00 1316 143 0.1934 0.2086 REMARK 3 3 3.3506 - 2.9274 1.00 1298 146 0.2243 0.2574 REMARK 3 4 2.9274 - 2.6599 1.00 1307 143 0.2358 0.2780 REMARK 3 5 2.6599 - 2.4693 1.00 1286 141 0.2326 0.2598 REMARK 3 6 2.4693 - 2.3238 1.00 1282 147 0.2422 0.3215 REMARK 3 7 2.3238 - 2.2075 1.00 1283 142 0.2433 0.2900 REMARK 3 8 2.2075 - 2.1114 0.99 1253 142 0.2537 0.2979 REMARK 3 9 2.1114 - 2.0301 0.94 1201 134 0.2559 0.2802 REMARK 3 10 2.0301 - 1.9601 0.80 1028 110 0.2869 0.3784 REMARK 3 11 1.9601 - 1.8988 0.56 713 71 0.2478 0.3122 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.002 1171 REMARK 3 ANGLE : 0.574 1591 REMARK 3 CHIRALITY : 0.044 192 REMARK 3 PLANARITY : 0.004 205 REMARK 3 DIHEDRAL : 12.856 698 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 5K1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221570. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100.15 REMARK 200 PH : 6.0-6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97960 REMARK 200 MONOCHROMATOR : DOUBLE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15873 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.899 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: 4F82 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M SODIUM ACETATE, 0.1 M TRIS-HCL, REMARK 280 0.2M SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 287.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.50267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.75133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.75133 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.50267 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 110.80650 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 63.97416 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 103.75667 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 237 LIES ON A SPECIAL POSITION. 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 LYS A 18 REMARK 465 GLU A 19 REMARK 465 GLY A 20 REMARK 465 MET A 21 REMARK 465 HIS A 160 REMARK 465 HIS A 161 REMARK 465 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 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 ALA A 51 -56.45 -130.88 REMARK 500 ALA A 91 56.99 -98.01 REMARK 500 ASP A 99 67.43 -116.90 REMARK 500 ALA A 115 -130.83 50.68 REMARK 500 GLU A 146 -38.41 -144.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5K2I RELATED DB: PDB REMARK 900 RELATED ID: 5K2J RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE REFERENCE DATABASE IS GENBANK ADV89163. THIS PROTEIN IS C48D/ REMARK 999 C73S MUTANT, AND RESIDUES 158-164 ARE EXPRESSION TAG. DBREF 5K1G A 1 164 PDB 5K1G 5K1G 1 164 SEQRES 1 A 164 MET ILE ALA GLN GLY GLN THR LEU PRO ASN ALA THR LEU SEQRES 2 A 164 SER GLN LEU THR LYS GLU GLY MET VAL HIS HIS PRO VAL SEQRES 3 A 164 LEU GLU LEU PHE ALA GLY LYS LYS VAL VAL LEU PHE ALA SEQRES 4 A 164 VAL PRO GLY ALA PHE THR PRO THR ASP SER GLU ALA HIS SEQRES 5 A 164 LEU PRO GLY TYR ILE VAL LEU ALA ASP GLN LEU LYS ALA SEQRES 6 A 164 LYS GLY VAL ASP LEU ILE ALA SER VAL SER VAL ASN ASP SEQRES 7 A 164 ALA PHE VAL MET LYS ALA TRP GLY GLU ALA GLN ASN ALA SEQRES 8 A 164 GLU GLU ILE LEU MET LEU ALA ASP GLY ASP ALA SER PHE SEQRES 9 A 164 THR LYS ALA LEU GLY LEU GLU MET ASP THR ALA GLY PHE SEQRES 10 A 164 GLY GLY LEU ARG SER GLN ARG TYR ALA MET ILE ILE ASP SEQRES 11 A 164 ASN GLY VAL VAL THR THR LEU ASN VAL GLU ALA PRO LYS SEQRES 12 A 164 SER PHE GLU VAL SER ASN ALA GLU THR ILE LEU ALA ALA SEQRES 13 A 164 LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *37(H2 O) HELIX 1 AA1 VAL A 26 PHE A 30 1 5 HELIX 2 AA2 THR A 45 ALA A 51 1 7 HELIX 3 AA3 ALA A 51 LEU A 59 1 9 HELIX 4 AA4 LEU A 59 LYS A 66 1 8 HELIX 5 AA5 ASP A 78 ASN A 90 1 13 HELIX 6 AA6 ALA A 102 GLY A 109 1 8 HELIX 7 AA7 ALA A 115 GLY A 118 5 4 HELIX 8 AA8 ASN A 149 HIS A 159 1 11 SHEET 1 AA1 2 THR A 12 SER A 14 0 SHEET 2 AA1 2 HIS A 23 PRO A 25 -1 O HIS A 24 N LEU A 13 SHEET 1 AA2 5 LEU A 95 ALA A 98 0 SHEET 2 AA2 5 LEU A 70 SER A 75 1 N SER A 73 O LEU A 97 SHEET 3 AA2 5 LYS A 34 ALA A 39 1 N VAL A 36 O ALA A 72 SHEET 4 AA2 5 TYR A 125 ASP A 130 -1 O MET A 127 N LEU A 37 SHEET 5 AA2 5 VAL A 133 VAL A 139 -1 O ASN A 138 N ALA A 126 SHEET 1 AA3 2 GLU A 111 ASP A 113 0 SHEET 2 AA3 2 LEU A 120 SER A 122 -1 O ARG A 121 N MET A 112 CRYST1 73.871 73.871 62.254 90.00 90.00 120.00 P 32 2 1 6 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 0.013537 0.007816 0.000000 0.00000 SCALE2 0.000000 0.015631 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016063 0.00000