HEADER OXIDOREDUCTASE 11-MAR-09 3GKM TITLE INSIGHTS INTO THE ALKYL PEROXIDE REDUCTION ACTIVITY OF XANTHOMONAS TITLE 2 CAMPESTRIS BACTERIOFERRITIN COMIGRATORY PROTEIN FROM THE TRAPPED TITLE 3 INTERMEDIATE/LIGAND COMPLEX STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOFERRITIN COMIGRATORY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 1.11.1.15; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS; SOURCE 3 ORGANISM_TAXID: 340; SOURCE 4 STRAIN: 17; SOURCE 5 GENE: BCP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS XANTHOMONAS CAMPESTRIS, BCP, PRX, ATYPICAL 2-CYS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.-J.LIAO REVDAT 5 01-NOV-23 3GKM 1 REMARK REVDAT 4 10-NOV-21 3GKM 1 REMARK SEQADV REVDAT 3 01-NOV-17 3GKM 1 REMARK REVDAT 2 03-NOV-09 3GKM 1 JRNL REVDAT 1 16-JUN-09 3GKM 0 JRNL AUTH S.-J.LIAO,C.-Y.YANG,K.-H.CHIN,A.H.-J.WANG,S.-H.CHOU JRNL TITL INSIGHTS INTO THE ALKYL PEROXIDE REDUCTION PATHWAY OF JRNL TITL 2 XANTHOMONAS CAMPESTRIS BACTERIOFERRITIN COMIGRATORY PROTEIN JRNL TITL 3 FROM THE TRAPPED INTERMEDIATE-LIGAND COMPLEX STRUCTURES JRNL REF J.MOL.BIOL. V. 390 951 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19477183 JRNL DOI 10.1016/J.JMB.2009.05.030 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 19523 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 994 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1193 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 247 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.44 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.269 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.022 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.575 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.845 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.577 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_REP.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3GKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051978. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 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 : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20772 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : 0.03300 REMARK 200 FOR THE DATA SET : 37.9080 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.12700 REMARK 200 R SYM FOR SHELL (I) : 0.12700 REMARK 200 FOR SHELL : 10.83 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3GKK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 36% PEG 4000, 0.1M CACODYLATE, PH 5.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 25.71050 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLN A 160 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 419 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GKK RELATED DB: PDB REMARK 900 RELATED ID: 3GKN RELATED DB: PDB DBREF 3GKM A 1 160 UNP Q8P9V9 Q8P9V9_XANCP 1 160 SEQADV 3GKM SER A -2 UNP Q8P9V9 EXPRESSION TAG SEQADV 3GKM ASN A -1 UNP Q8P9V9 EXPRESSION TAG SEQADV 3GKM ALA A 0 UNP Q8P9V9 EXPRESSION TAG SEQADV 3GKM SER A 48 UNP Q8P9V9 CYS 48 ENGINEERED MUTATION SEQADV 3GKM SER A 84 UNP Q8P9V9 CYS 84 ENGINEERED MUTATION SEQRES 1 A 163 SER ASN ALA MET THR ASP ALA VAL LEU GLU LEU PRO ALA SEQRES 2 A 163 ALA THR PHE ASP LEU PRO LEU SER LEU SER GLY GLY THR SEQRES 3 A 163 GLN THR THR LEU ARG ALA HIS ALA GLY HIS TRP LEU VAL SEQRES 4 A 163 ILE TYR PHE TYR PRO LYS ASP SER THR PRO GLY SER THR SEQRES 5 A 163 THR GLU GLY LEU ASP PHE ASN ALA LEU LEU PRO GLU PHE SEQRES 6 A 163 ASP LYS ALA GLY ALA LYS ILE LEU GLY VAL SER ARG ASP SEQRES 7 A 163 SER VAL LYS SER HIS ASP ASN PHE SER ALA LYS GLN GLY SEQRES 8 A 163 PHE ALA PHE PRO LEU VAL SER ASP GLY ASP GLU ALA LEU SEQRES 9 A 163 CYS ARG ALA PHE ASP VAL ILE LYS GLU LYS ASN MET TYR SEQRES 10 A 163 GLY LYS GLN VAL LEU GLY ILE GLU ARG SER THR PHE LEU SEQRES 11 A 163 LEU SER PRO GLU GLY GLN VAL VAL GLN ALA TRP ARG LYS SEQRES 12 A 163 VAL LYS VAL ALA GLY HIS ALA ASP ALA VAL LEU ALA ALA SEQRES 13 A 163 LEU LYS ALA HIS ALA LYS GLN HET FMT A 408 3 HET FMT A 409 3 HET FMT A 410 3 HET FMT A 411 3 HET FMT A 412 3 HET FMT A 413 3 HET FMT A 414 3 HET FMT A 415 3 HET FMT A 416 3 HET FMT A 417 3 HET FMT A 418 3 HET FMT A 419 3 HETNAM FMT FORMIC ACID FORMUL 2 FMT 12(C H2 O2) FORMUL 14 HOH *247(H2 O) HELIX 1 1 PRO A 9 LEU A 15 5 7 HELIX 2 2 LEU A 27 ALA A 31 5 5 HELIX 3 3 THR A 45 LEU A 58 1 14 HELIX 4 4 LEU A 58 ALA A 65 1 8 HELIX 5 5 SER A 76 GLY A 88 1 13 HELIX 6 6 GLU A 99 PHE A 105 1 7 HELIX 7 7 GLY A 145 LYS A 159 1 15 SHEET 1 A 7 GLN A 24 THR A 25 0 SHEET 2 A 7 LEU A 17 LEU A 19 -1 N LEU A 17 O THR A 25 SHEET 3 A 7 LEU A 93 SER A 95 -1 O SER A 95 N SER A 18 SHEET 4 A 7 LYS A 68 SER A 73 1 N GLY A 71 O VAL A 94 SHEET 5 A 7 LEU A 35 PHE A 39 1 N VAL A 36 O LYS A 68 SHEET 6 A 7 SER A 124 LEU A 128 -1 O SER A 124 N PHE A 39 SHEET 7 A 7 VAL A 134 ARG A 139 -1 O TRP A 138 N THR A 125 SHEET 1 B 2 ILE A 108 MET A 113 0 SHEET 2 B 2 LYS A 116 ILE A 121 -1 O VAL A 118 N LYS A 111 SITE 1 AC1 2 ALA A 90 HOH A 391 SITE 1 AC2 5 VAL A 5 LEU A 6 ALA A 137 ARG A 139 SITE 2 AC2 5 HOH A 347 SITE 1 AC3 5 SER A 18 SER A 95 GLY A 97 HOH A 269 SITE 2 AC3 5 FMT A 415 SITE 1 AC4 6 PRO A 41 LYS A 42 THR A 45 SER A 48 SITE 2 AC4 6 ARG A 123 HOH A 396 SITE 1 AC5 3 ALA A 10 HOH A 201 FMT A 413 SITE 1 AC6 4 PRO A 9 ALA A 10 HOH A 240 FMT A 412 SITE 1 AC7 6 ALA A 137 HOH A 174 HOH A 220 HOH A 244 SITE 2 AC7 6 HOH A 288 HOH A 366 SITE 1 AC8 5 SER A 76 HOH A 165 HOH A 297 HOH A 394 SITE 2 AC8 5 FMT A 410 SITE 1 AC9 4 LEU A 6 GLU A 7 HOH A 320 HOH A 331 SITE 1 BC1 4 SER A 20 PRO A 92 HOH A 233 HOH A 393 SITE 1 BC2 3 ALA A 29 HIS A 33 HOH A 276 SITE 1 BC3 4 GLU A 99 LEU A 119 GLY A 120 HOH A 401 CRYST1 35.397 51.421 39.844 90.00 103.24 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 0.028251 0.000000 0.006649 0.00000 SCALE2 0.000000 0.019447 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025784 0.00000