HEADER OXIDOREDUCTASE 09-MAR-16 5IOX TITLE XANTHOMONAS CAMPESTRIS PEROXIREDOXIN Q - STRUCTURE LUSS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOFERRITIN COMIGRATORY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS (STRAIN SOURCE 3 ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25); SOURCE 4 ORGANISM_TAXID: 190485; SOURCE 5 STRAIN: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25; SOURCE 6 GENE: XCC1738; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PRXQ, BCP, PEROXIDASE, REDOX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.PERKINS,D.PARSONAGE,K.J.NELSON,L.B.POOLE,A.KARPLUS REVDAT 4 27-SEP-23 5IOX 1 REMARK REVDAT 3 22-NOV-17 5IOX 1 JRNL REMARK REVDAT 2 19-OCT-16 5IOX 1 JRNL REVDAT 1 21-SEP-16 5IOX 0 JRNL AUTH A.PERKINS,D.PARSONAGE,K.J.NELSON,O.M.OGBA,P.H.CHEONG, JRNL AUTH 2 L.B.POOLE,P.A.KARPLUS JRNL TITL PEROXIREDOXIN CATALYSIS AT ATOMIC RESOLUTION. JRNL REF STRUCTURE V. 24 1668 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27594682 JRNL DOI 10.1016/J.STR.2016.07.012 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 28974 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1481 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 33.0167 - 3.5274 0.99 2915 172 0.1457 0.1678 REMARK 3 2 3.5274 - 2.8003 0.97 2852 170 0.1557 0.2180 REMARK 3 3 2.8003 - 2.4464 0.97 2812 182 0.1697 0.1842 REMARK 3 4 2.4464 - 2.2228 0.97 2913 154 0.1588 0.1930 REMARK 3 5 2.2228 - 2.0635 0.98 2919 135 0.1674 0.1864 REMARK 3 6 2.0635 - 1.9419 0.98 2904 152 0.1681 0.2046 REMARK 3 7 1.9419 - 1.8446 0.98 2894 160 0.1848 0.2282 REMARK 3 8 1.8446 - 1.7643 0.98 2899 157 0.1887 0.2261 REMARK 3 9 1.7643 - 1.6964 0.98 2880 144 0.2033 0.2430 REMARK 3 10 1.6964 - 1.6379 0.97 2870 145 0.2113 0.2249 REMARK 3 11 1.6379 - 1.5867 0.97 2906 150 0.2032 0.2524 REMARK 3 12 1.5867 - 1.5413 0.97 2873 167 0.2126 0.2524 REMARK 3 13 1.5413 - 1.5007 0.97 2830 174 0.2349 0.2882 REMARK 3 14 1.5007 - 1.4641 0.97 2836 179 0.2624 0.3276 REMARK 3 15 1.4641 - 1.4308 0.92 2767 118 0.3016 0.3263 REMARK 3 16 1.4308 - 1.4004 0.86 2515 131 0.3286 0.3354 REMARK 3 17 1.4004 - 1.3724 0.77 2298 122 0.3389 0.3886 REMARK 3 18 1.3724 - 1.3465 0.66 2003 83 0.3568 0.4063 REMARK 3 19 1.3465 - 1.3224 0.57 1698 76 0.3664 0.3573 REMARK 3 20 1.3224 - 1.3000 0.48 1426 76 0.3826 0.3687 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.210 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 : 0.009 1220 REMARK 3 ANGLE : 1.296 1654 REMARK 3 CHIRALITY : 0.081 187 REMARK 3 PLANARITY : 0.006 214 REMARK 3 DIHEDRAL : 13.508 435 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 5IOX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219210. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96486 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28974 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 34.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3GKK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M AMMONIUM SULFATE, 0.2 M SODIUM REMARK 280 CHLORIDE, 0.1 M SODIUM CACODYLATE PH 6.8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 300K 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 27.06500 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 1 REMARK 465 THR A 2 REMARK 465 SER A 79 REMARK 465 HIS A 80 REMARK 465 GLN A 160 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 78 CG CD CE NZ 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 O HOH A 223 O HOH A 251 2.13 REMARK 500 O HOH A 213 O HOH A 304 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IIZ RELATED DB: PDB REMARK 900 RELATED ID: 5IM9 RELATED DB: PDB REMARK 900 RELATED ID: 5IMA RELATED DB: PDB REMARK 900 RELATED ID: 5IMC RELATED DB: PDB REMARK 900 RELATED ID: 5IMD RELATED DB: PDB REMARK 900 RELATED ID: 5IMF RELATED DB: PDB REMARK 900 RELATED ID: 5IMV RELATED DB: PDB REMARK 900 RELATED ID: 5IMZ RELATED DB: PDB REMARK 900 RELATED ID: 5INY RELATED DB: PDB REMARK 900 RELATED ID: 5IO0 RELATED DB: PDB REMARK 900 RELATED ID: 5IO2 RELATED DB: PDB REMARK 900 RELATED ID: 5IOW RELATED DB: PDB REMARK 900 RELATED ID: 5IPG RELATED DB: PDB REMARK 900 RELATED ID: 5IPH RELATED DB: PDB DBREF 5IOX A 1 160 UNP Q8P9V9 Q8P9V9_XANCP 1 160 SEQRES 1 A 160 MET THR ASP ALA VAL LEU GLU LEU PRO ALA ALA THR PHE SEQRES 2 A 160 ASP LEU PRO LEU SER LEU SER GLY GLY THR GLN THR THR SEQRES 3 A 160 LEU ARG ALA HIS ALA GLY HIS TRP LEU VAL ILE TYR PHE SEQRES 4 A 160 TYR PRO LYS ASP SER THR PRO GLY CYS THR THR GLU GLY SEQRES 5 A 160 LEU ASP PHE ASN ALA LEU LEU PRO GLU PHE ASP LYS ALA SEQRES 6 A 160 GLY ALA LYS ILE LEU GLY VAL SER ARG ASP SER VAL LYS SEQRES 7 A 160 SER HIS ASP ASN PHE CYS ALA LYS GLN GLY PHE ALA PHE SEQRES 8 A 160 PRO LEU VAL SER ASP GLY ASP GLU ALA LEU CYS ARG ALA SEQRES 9 A 160 PHE ASP VAL ILE LYS GLU LYS ASN MET TYR GLY LYS GLN SEQRES 10 A 160 VAL LEU GLY ILE GLU ARG SER THR PHE LEU LEU SER PRO SEQRES 11 A 160 GLU GLY GLN VAL VAL GLN ALA TRP ARG LYS VAL LYS VAL SEQRES 12 A 160 ALA GLY HIS ALA ASP ALA VAL LEU ALA ALA LEU LYS ALA SEQRES 13 A 160 HIS ALA LYS GLN FORMUL 2 HOH *125(H2 O) HELIX 1 AA1 PRO A 9 LEU A 15 5 7 HELIX 2 AA2 THR A 26 ALA A 31 5 6 HELIX 3 AA3 SER A 44 ALA A 65 1 22 HELIX 4 AA4 CYS A 84 GLY A 88 5 5 HELIX 5 AA5 GLU A 99 PHE A 105 1 7 HELIX 6 AA6 GLY A 145 LYS A 159 1 15 SHEET 1 AA1 7 GLN A 24 THR A 25 0 SHEET 2 AA1 7 LEU A 17 LEU A 19 -1 N LEU A 17 O THR A 25 SHEET 3 AA1 7 LEU A 93 SER A 95 -1 O SER A 95 N SER A 18 SHEET 4 AA1 7 ALA A 67 SER A 73 1 N GLY A 71 O VAL A 94 SHEET 5 AA1 7 TRP A 34 PHE A 39 1 N TYR A 38 O VAL A 72 SHEET 6 AA1 7 SER A 124 LEU A 128 -1 O SER A 124 N PHE A 39 SHEET 7 AA1 7 VAL A 134 ARG A 139 -1 O GLN A 136 N LEU A 127 SHEET 1 AA2 2 ILE A 108 MET A 113 0 SHEET 2 AA2 2 LYS A 116 ILE A 121 -1 O LYS A 116 N MET A 113 SSBOND 1 CYS A 48 CYS A 84 1555 1555 2.03 CRYST1 34.650 54.130 36.610 90.00 107.72 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 0.028860 0.000000 0.009222 0.00000 SCALE2 0.000000 0.018474 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028675 0.00000