HEADER OXIDOREDUCTASE 11-JUL-12 4G2E TITLE CRYSTAL STRUCTURE OF A DIMERIC PRXQ FROM SULFOLOBUS TOKODAII COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXIREDOXIN; COMPND 3 CHAIN: A; COMPND 4 EC: 1.11.1.15; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS TOKODAII; SOURCE 3 ORGANISM_TAXID: 273063; SOURCE 4 STRAIN: DSM 16993 / JCM 10545 / NBRC 100140 / 7; SOURCE 5 GENE: BCP4, STK_17850; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS REDOX PROTEIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 2 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, DIMER, A-TYPE, LU, LOCALLY KEYWDS 4 UNFOLDED, PEROXIREDOXIN, PRXQ, DISULFIDE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.PERKINS,M.C.GRETES,P.A.KARPLUS REVDAT 3 13-SEP-23 4G2E 1 SEQADV REVDAT 2 20-FEB-13 4G2E 1 JRNL REVDAT 1 24-OCT-12 4G2E 0 JRNL AUTH A.PERKINS,M.C.GRETES,K.J.NELSON,L.B.POOLE,P.A.KARPLUS JRNL TITL MAPPING THE ACTIVE SITE HELIX-TO-STRAND CONVERSION OF CXXXXC JRNL TITL 2 PEROXIREDOXIN Q ENZYMES. JRNL REF BIOCHEMISTRY V. 51 7638 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22928725 JRNL DOI 10.1021/BI301017S REMARK 0 REMARK 0 THIS ENTRY 4G2E REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 STRUCTURAL DATA (R2YWNSF) DETERMINED BY AUTHORS OF THE PDB ENTRY REMARK 0 2YWN: A.EBIHARA, M.MANZOKU, Y.FUJIMOTO, S.YOKOYAMA, S.KURAMITSU, REMARK 0 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.3 REMARK 3 NUMBER OF REFLECTIONS : 29551 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 2792 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 26.6195 - 3.7967 0.99 3037 182 0.1447 0.1489 REMARK 3 2 3.7967 - 3.0149 1.00 3027 184 0.1223 0.1393 REMARK 3 3 3.0149 - 2.6342 1.00 3072 141 0.1208 0.1427 REMARK 3 4 2.6342 - 2.3935 1.00 3073 161 0.1098 0.1361 REMARK 3 5 2.3935 - 2.2221 1.00 3084 147 0.1021 0.1362 REMARK 3 6 2.2221 - 2.0911 1.00 3049 170 0.0978 0.1423 REMARK 3 7 2.0911 - 1.9864 1.00 3069 155 0.1034 0.1607 REMARK 3 8 1.9864 - 1.9000 1.00 3045 174 0.1020 0.1414 REMARK 3 9 1.9000 - 1.8268 1.00 3084 166 0.0930 0.1390 REMARK 3 10 1.8268 - 1.7638 1.00 3018 154 0.1006 0.1360 REMARK 3 11 1.7638 - 1.7087 1.00 3081 162 0.0991 0.1546 REMARK 3 12 1.7087 - 1.6598 1.00 3055 183 0.1104 0.1538 REMARK 3 13 1.6598 - 1.6161 0.97 2988 151 0.1163 0.1574 REMARK 3 14 1.6161 - 1.5767 0.87 2663 131 0.1152 0.1927 REMARK 3 15 1.5767 - 1.5409 0.79 2391 127 0.1337 0.1997 REMARK 3 16 1.5409 - 1.5081 0.70 2136 116 0.1512 0.1915 REMARK 3 17 1.5081 - 1.4779 0.64 1981 82 0.1719 0.2016 REMARK 3 18 1.4779 - 1.4500 0.57 1741 74 0.1782 0.1991 REMARK 3 19 1.4500 - 1.4241 0.50 1569 86 0.2023 0.2160 REMARK 3 20 1.4241 - 1.4000 0.42 1282 46 0.2427 0.3384 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 47.27 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.35410 REMARK 3 B22 (A**2) : 0.51640 REMARK 3 B33 (A**2) : -1.87050 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 : 0.008 1279 REMARK 3 ANGLE : 1.137 1738 REMARK 3 CHIRALITY : 0.071 191 REMARK 3 PLANARITY : 0.008 223 REMARK 3 DIHEDRAL : 11.628 483 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 4G2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073651. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2YWN REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 2YWN. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.97750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.97750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 34.66850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.32650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.66850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.32650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.97750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.66850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.32650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.97750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.66850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.32650 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 61.95500 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 A1155 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1207 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 CYS A 44 REMARK 465 THR A 45 REMARK 465 LYS A 46 REMARK 465 GLU A 47 REMARK 465 MET A 48 REMARK 465 CYS A 49 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 HH12 ARG A 118 O HOH A 1052 1.38 REMARK 500 HE ARG A 118 O HOH A 1055 1.50 REMARK 500 O HOH A 1080 O HOH A 1114 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YWN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PEROXIREDOXIN-LIKE PROTEIN FROM SULFOLOBUS REMARK 900 TOKODAII. THIS ENTRY 4G2E REFLECTS AN ALTERNATIVE MODELING OF X-RAY REMARK 900 DATA R2YWNSF. REMARK 900 RELATED ID: 2CX3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A BACTERIOFERRITIN COMIGRATORY PROTEIN REMARK 900 PEROXIREDOXIN FROM THE AEROPYRUM PERNIX K1 (FORM-1 CRYSTAL) REMARK 900 RELATED ID: 2CX4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A BACTERIOFERRITIN COMIGRATORY PROTEIN REMARK 900 PEROXIREDOXIN FROM THE AEROPYRUM PERNIX K1 (FORM-2 CRYSTAL) REMARK 900 RELATED ID: 2GQC RELATED DB: PDB REMARK 900 RELATED ID: 2GQF RELATED DB: PDB DBREF 4G2E A 1 155 UNP F9VNL8 F9VNL8_SULTO 1 155 SEQADV 4G2E GLY A -2 UNP F9VNL8 EXPRESSION TAG SEQADV 4G2E HIS A -1 UNP F9VNL8 EXPRESSION TAG SEQRES 1 A 157 GLY HIS MET VAL GLU ILE GLY GLU LEU ALA PRO ASP PHE SEQRES 2 A 157 GLU LEU PRO ASP THR GLU LEU LYS LYS VAL LYS LEU SER SEQRES 3 A 157 ALA LEU LYS GLY LYS VAL VAL VAL LEU ALA PHE TYR PRO SEQRES 4 A 157 ALA ALA PHE THR GLN VAL CYS THR LYS GLU MET CYS THR SEQRES 5 A 157 PHE ARG ASP SER MET ALA LYS PHE ASN GLN VAL ASN ALA SEQRES 6 A 157 VAL VAL LEU GLY ILE SER VAL ASP PRO PRO PHE SER ASN SEQRES 7 A 157 LYS ALA PHE LYS GLU HIS ASN LYS LEU ASN PHE THR ILE SEQRES 8 A 157 LEU SER ASP TYR ASN ARG GLU VAL VAL LYS LYS TYR ASN SEQRES 9 A 157 VAL ALA TRP GLU PHE PRO ALA LEU PRO GLY TYR VAL LEU SEQRES 10 A 157 ALA LYS ARG ALA VAL PHE VAL ILE ASP LYS GLU GLY LYS SEQRES 11 A 157 VAL ARG TYR LYS TRP VAL SER ASP ASP PRO THR LYS GLU SEQRES 12 A 157 PRO PRO TYR ASP GLU ILE GLU LYS VAL VAL LYS SER LEU SEQRES 13 A 157 SER FORMUL 2 HOH *305(H2 O) HELIX 1 1 SER A 24 LYS A 27 5 4 HELIX 2 2 ASP A 53 VAL A 61 5 9 HELIX 3 3 PRO A 72 ASN A 83 1 12 HELIX 4 4 ARG A 95 TYR A 101 1 7 HELIX 5 5 PRO A 143 LEU A 154 1 12 SHEET 1 A 2 GLU A 12 PRO A 14 0 SHEET 2 A 2 LYS A 20 LYS A 22 -1 O VAL A 21 N LEU A 13 SHEET 1 B 5 THR A 88 SER A 91 0 SHEET 2 B 5 VAL A 64 SER A 69 1 N GLY A 67 O LEU A 90 SHEET 3 B 5 VAL A 31 PHE A 35 1 N VAL A 32 O LEU A 66 SHEET 4 B 5 ARG A 118 ILE A 123 -1 O ILE A 123 N VAL A 31 SHEET 5 B 5 VAL A 129 SER A 135 -1 O ARG A 130 N VAL A 122 SHEET 1 C 2 ALA A 104 GLU A 106 0 SHEET 2 C 2 VAL A 114 ALA A 116 -1 O LEU A 115 N TRP A 105 CRYST1 69.337 78.653 61.955 90.00 90.00 90.00 C 2 2 21 8 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 0.014422 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016141 0.00000