HEADER IMMUNE SYSTEM 28-APR-06 2GU9 TITLE CRYSTAL STRUCTURE OF XC5357 FROM XANTHOMONAS CAMPESTRIS: A PUTATIVE TITLE 2 TETRACENOMYCIN POLYKETIDE SYNTHESIS PROTEIN ADOPTING A NOVEL CUPIN TITLE 3 SUBFAMILY STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETRACENOMYCIN POLYKETIDE SYNTHESIS PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS CAMPESTRIS; SOURCE 3 ORGANISM_TAXID: 339; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS XANTHOMONAS CAMPESTRIS, CUPIN, TETRACENOMYCIN POLYKETIDE, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.-H.CHIN,C.C.CHOU,A.H.-J.WANG,S.-H.CHOU REVDAT 4 13-MAR-24 2GU9 1 REMARK REVDAT 3 24-FEB-09 2GU9 1 VERSN REVDAT 2 28-NOV-06 2GU9 1 JRNL REVDAT 1 07-NOV-06 2GU9 0 JRNL AUTH K.-H.CHIN,C.C.CHOU,A.H.-J.WANG,S.-H.CHOU JRNL TITL CRYSTAL STRUCTURE OF XC5357 FROM XANTHOMONAS CAMPESTRIS: A JRNL TITL 2 PUTATIVE TETRACENOMYCIN POLYKETIDE SYNTHESIS PROTEIN JRNL TITL 3 ADOPTING A NOVEL CUPIN SUBFAMILY STRUCTURE JRNL REF PROTEINS V. 65 1046 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 17029242 JRNL DOI 10.1002/PROT.21142 REMARK 2 REMARK 2 RESOLUTION. 1.40 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 32312 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RADOM REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2854 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL 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 (%) : NULL 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 : 1681 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : 0.020 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037556. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-05; 02-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 12 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8 REMARK 200 BEAMLINE : BL12B2; BL12B2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97963, 0.96389; 0.97963 REMARK 200 MONOCHROMATOR : SE-MET; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32312 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 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) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 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: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NAOAC, 1.6M LISO4, PH 5.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 2810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 113 REMARK 465 MET B 1 REMARK 465 GLU B 112 REMARK 465 GLY B 113 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 LEU A 15 N REMARK 470 GLN B 2 CB 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 PHE A 12 113.09 -163.87 REMARK 500 ARG A 19 59.92 38.53 REMARK 500 ASP A 38 -139.52 -120.24 REMARK 500 HIS A 41 -159.69 -114.70 REMARK 500 ASP A 60 -119.70 63.09 REMARK 500 PHE B 12 114.63 -160.89 REMARK 500 LEU B 15 -69.64 -91.78 REMARK 500 ARG B 19 59.57 37.82 REMARK 500 ASP B 38 -136.92 -129.55 REMARK 500 HIS B 41 -158.22 -114.12 REMARK 500 ASP B 60 -36.14 61.79 REMARK 500 REMARK 500 REMARK: NULL DBREF 2GU9 A 1 113 UNP Q8PBM3 Q8PBM3_XANCP 1 113 DBREF 2GU9 B 1 113 UNP Q8PBM3 Q8PBM3_XANCP 1 113 SEQRES 1 A 113 MET GLN TYR ALA THR LEU GLU LEU ASN ASN ALA PHE LYS SEQRES 2 A 113 VAL LEU PHE SER LEU ARG GLN VAL GLN ALA ALA GLU MET SEQRES 3 A 113 VAL ILE ALA PRO GLY ASP ARG GLU GLY GLY PRO ASP ASN SEQRES 4 A 113 ARG HIS ARG GLY ALA ASP GLN TRP LEU PHE VAL VAL ASP SEQRES 5 A 113 GLY ALA GLY GLU ALA ILE VAL ASP GLY HIS THR GLN ALA SEQRES 6 A 113 LEU GLN ALA GLY SER LEU ILE ALA ILE GLU ARG GLY GLN SEQRES 7 A 113 ALA HIS GLU ILE ARG ASN THR GLY ASP THR PRO LEU LYS SEQRES 8 A 113 THR VAL ASN PHE TYR HIS PRO PRO ALA TYR ASP ALA GLN SEQRES 9 A 113 GLY GLU PRO LEU PRO ALA GLY GLU GLY SEQRES 1 B 113 MET GLN TYR ALA THR LEU GLU LEU ASN ASN ALA PHE LYS SEQRES 2 B 113 VAL LEU PHE SER LEU ARG GLN VAL GLN ALA ALA GLU MET SEQRES 3 B 113 VAL ILE ALA PRO GLY ASP ARG GLU GLY GLY PRO ASP ASN SEQRES 4 B 113 ARG HIS ARG GLY ALA ASP GLN TRP LEU PHE VAL VAL ASP SEQRES 5 B 113 GLY ALA GLY GLU ALA ILE VAL ASP GLY HIS THR GLN ALA SEQRES 6 B 113 LEU GLN ALA GLY SER LEU ILE ALA ILE GLU ARG GLY GLN SEQRES 7 B 113 ALA HIS GLU ILE ARG ASN THR GLY ASP THR PRO LEU LYS SEQRES 8 B 113 THR VAL ASN PHE TYR HIS PRO PRO ALA TYR ASP ALA GLN SEQRES 9 B 113 GLY GLU PRO LEU PRO ALA GLY GLU GLY SHEET 1 A 6 TYR A 3 THR A 5 0 SHEET 2 A 6 SER B 70 ILE B 74 -1 O LEU B 71 N ALA A 4 SHEET 3 A 6 ASP B 45 ASP B 52 -1 N GLN B 46 O ILE B 74 SHEET 4 A 6 LEU B 90 HIS B 97 -1 O HIS B 97 N ASP B 45 SHEET 5 A 6 VAL B 21 ILE B 28 -1 N ALA B 24 O ASN B 94 SHEET 6 A 6 PHE B 12 LEU B 18 -1 N LYS B 13 O GLU B 25 SHEET 1 B 6 LYS A 13 LEU A 18 0 SHEET 2 B 6 VAL A 21 ILE A 28 -1 O GLU A 25 N LYS A 13 SHEET 3 B 6 LEU A 90 HIS A 97 -1 O ASN A 94 N ALA A 24 SHEET 4 B 6 ASP A 45 ASP A 52 -1 N ASP A 45 O HIS A 97 SHEET 5 B 6 SER A 70 ILE A 74 -1 O ILE A 74 N GLN A 46 SHEET 6 B 6 TYR B 3 THR B 5 -1 O ALA B 4 N LEU A 71 SHEET 1 C 4 ARG A 33 GLY A 35 0 SHEET 2 C 4 HIS A 80 ARG A 83 -1 O ILE A 82 N GLU A 34 SHEET 3 C 4 GLY A 55 VAL A 59 -1 N ILE A 58 O GLU A 81 SHEET 4 C 4 HIS A 62 LEU A 66 -1 O LEU A 66 N GLY A 55 SHEET 1 D 4 ARG B 33 GLU B 34 0 SHEET 2 D 4 HIS B 80 ASN B 84 -1 O ILE B 82 N GLU B 34 SHEET 3 D 4 GLY B 55 VAL B 59 -1 N GLU B 56 O ARG B 83 SHEET 4 D 4 HIS B 62 LEU B 66 -1 O LEU B 66 N GLY B 55 CISPEP 1 HIS A 97 PRO A 98 0 -0.34 CISPEP 2 HIS B 97 PRO B 98 0 -0.29 CRYST1 43.700 43.680 46.500 65.00 64.90 73.40 P 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 0.022883 -0.006822 -0.008904 0.00000 SCALE2 0.000000 0.023889 -0.008849 0.00000 SCALE3 0.000000 0.000000 0.025325 0.00000