HEADER PROTEIN BINDING/MEMBRANE PROTEIN 21-JUN-12 4FOU TITLE STRUCTURE OF THE PILZ-FIMX(EAL DOMAIN)-C-DI-GMP COMPLEX RESPONSIBLE TITLE 2 FOR THE REGULATION OF BACTERIAL TYPE IV PILUS BIOGENESIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIMX; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EAL DOMAIN (UNP RESIDUES 426-689); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TYPE IV FIMBRIAE ASSEMBLY PROTEIN; COMPND 8 CHAIN: D, C; COMPND 9 SYNONYM: PILZ; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS AXONOPODIS PV. CITRI; SOURCE 3 ORGANISM_TAXID: 190486; SOURCE 4 STRAIN: 306; SOURCE 5 GENE: XAC2398; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: XANTHOMONAS AXONOPODIS PV. CITRI; SOURCE 13 ORGANISM_TAXID: 190486; SOURCE 14 STRAIN: 306; SOURCE 15 GENE: PILZ, XAC1133; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS BACTERIAL TYPE 4 PILUS BIOGENESIS REGULATION, PROTEIN BINDING- KEYWDS 2 MEMBRANE PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.S.FARAH,C.R.GUZZO REVDAT 4 28-FEB-24 4FOU 1 REMARK HETSYN LINK REVDAT 3 12-JUN-13 4FOU 1 JRNL REVDAT 2 03-APR-13 4FOU 1 JRNL REVDAT 1 27-MAR-13 4FOU 0 JRNL AUTH C.R.GUZZO,G.DUNGER,R.K.SALINAS,C.S.FARAH JRNL TITL STRUCTURE OF THE PILZ-FIMXEAL-C-DI-GMP COMPLEX RESPONSIBLE JRNL TITL 2 FOR THE REGULATION OF BACTERIAL TYPE IV PILUS BIOGENESIS. JRNL REF J.MOL.BIOL. V. 425 2174 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23507310 JRNL DOI 10.1016/J.JMB.2013.03.021 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 54199 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 + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2858 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3977 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 201 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5559 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 363 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.71000 REMARK 3 B22 (A**2) : -0.71000 REMARK 3 B33 (A**2) : 1.06000 REMARK 3 B12 (A**2) : -0.35000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.121 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.457 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6099 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4177 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8335 ; 1.529 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10165 ; 0.929 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 779 ; 6.014 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 289 ;36.679 ;23.633 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1004 ;16.348 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 51 ;19.003 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 904 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6877 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1284 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3693 ; 1.003 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1494 ; 0.209 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5958 ; 1.812 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2406 ; 2.392 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2353 ; 3.718 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4FOU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000073168. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.459 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57146 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.860 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG4000, 0.1 M TRIS, PH 7.5, 0.2 M REMARK 280 CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 71.54467 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 35.77233 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 53.65850 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 17.88617 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 89.43083 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 REMARK 350 BIOMOLECULE: 2 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: 3420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 VAL A 426 REMARK 465 SER A 427 REMARK 465 VAL B 426 REMARK 465 SER B 427 REMARK 465 ILE B 428 REMARK 465 MET D 1 REMARK 465 SER D 2 REMARK 465 ALA D 3 REMARK 465 MET D 4 REMARK 465 ASN D 5 REMARK 465 GLY D 74 REMARK 465 ALA D 75 REMARK 465 GLN D 76 REMARK 465 GLY D 77 REMARK 465 ASN D 78 REMARK 465 ARG D 79 REMARK 465 LEU D 107 REMARK 465 THR D 108 REMARK 465 THR D 109 REMARK 465 SER D 110 REMARK 465 ASP D 111 REMARK 465 LYS D 112 REMARK 465 PRO D 113 REMARK 465 THR D 114 REMARK 465 HIS D 115 REMARK 465 THR D 116 REMARK 465 MET D 117 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 ALA C 3 REMARK 465 MET C 4 REMARK 465 ASN C 5 REMARK 465 ALA C 6 REMARK 465 ARG C 7 REMARK 465 ALA C 73 REMARK 465 GLY C 74 REMARK 465 ALA C 75 REMARK 465 GLN C 76 REMARK 465 GLY C 77 REMARK 465 ASN C 78 REMARK 465 THR C 109 REMARK 465 SER C 110 REMARK 465 ASP C 111 REMARK 465 LYS C 112 REMARK 465 PRO C 113 REMARK 465 THR C 114 REMARK 465 HIS C 115 REMARK 465 THR C 116 REMARK 465 MET C 117 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 ARG C 79 CG CD NE CZ NH1 NH2 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 VAL A 454 -75.33 -77.09 REMARK 500 ALA A 678 146.02 -178.16 REMARK 500 ALA B 678 142.46 -174.93 REMARK 500 ARG D 7 -50.19 -121.16 REMARK 500 THR C 38 134.03 -174.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 703 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 435 OD1 REMARK 620 2 HOH A 948 O 92.0 REMARK 620 3 GLU B 440 OE2 173.0 83.8 REMARK 620 4 HOH B 876 O 98.6 114.7 78.1 REMARK 620 5 HOH B 877 O 97.0 90.7 88.8 149.5 REMARK 620 6 HOH B 878 O 93.9 154.2 92.4 89.2 63.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 702 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 502 O REMARK 620 2 ASP A 502 OD2 79.9 REMARK 620 3 GLU A 506 OE2 112.5 162.7 REMARK 620 4 GLU A 506 OE1 75.7 148.9 48.5 REMARK 620 5 HOH A 810 O 142.9 99.4 78.1 88.8 REMARK 620 6 HOH A 939 O 67.1 82.9 90.8 104.7 150.0 REMARK 620 7 HOH A 971 O 88.2 69.4 121.2 90.6 58.0 145.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 705 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 938 O REMARK 620 2 GLU B 440 OE1 142.8 REMARK 620 3 GLU B 443 OE1 90.4 95.6 REMARK 620 4 HOH B 879 O 72.9 70.0 103.5 REMARK 620 5 HOH B 880 O 57.7 157.7 92.2 128.2 REMARK 620 6 HOH C 225 O 145.1 70.9 94.9 138.1 87.6 REMARK 620 7 HOH C 226 O 83.4 95.2 168.4 84.1 76.2 84.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 705 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CNR RELATED DB: PDB REMARK 900 XANTHOMONAS AXONOPODIS PV CITRI PILZ (XAC1133) REMARK 900 RELATED ID: 4FOJ RELATED DB: PDB REMARK 900 1.55 A CRYSTAL STRUCTURE OF XANTHOMONAS CITRI FIMX EAL DOMAIN IN REMARK 900 COMPLEX WITH C-DIGMP REMARK 900 RELATED ID: 4FOK RELATED DB: PDB REMARK 900 1.8 A CRYSTAL STRUCTURE OF THE FIMX EAL DOMAIN IN COMPLEX WITH C- REMARK 900 DIGMP DBREF 4FOU A 426 689 UNP Q8PJX9 Q8PJX9_XANAC 426 689 DBREF 4FOU B 426 689 UNP Q8PJX9 Q8PJX9_XANAC 426 689 DBREF 4FOU D 1 117 UNP Q8PND9 Q8PND9_XANAC 1 117 DBREF 4FOU C 1 117 UNP Q8PND9 Q8PND9_XANAC 1 117 SEQRES 1 A 264 VAL SER ILE TYR ASP PRO ALA ALA ALA ASP ARG ALA GLU SEQRES 2 A 264 GLU GLU ARG ILE GLU ARG TRP VAL GLU GLN LEU ARG GLU SEQRES 3 A 264 ALA LEU VAL GLY ASP GLY PHE LEU LEU HIS TYR GLN PRO SEQRES 4 A 264 VAL LEU ASN LEU GLN GLY GLU PRO LEU GLU LEU TYR GLN SEQRES 5 A 264 ALA PHE LEU ARG LEU GLU ARG ASN GLY GLU MET MET SER SEQRES 6 A 264 PRO ASN ALA PHE MET ALA ILE ALA GLU GLU HIS ASP LEU SEQRES 7 A 264 VAL THR GLU ILE ASP ARG TRP VAL VAL ALA ARG ALA ILE SEQRES 8 A 264 ARG GLN LEU GLY GLU ARG GLN ARG ALA GLY HIS LYS THR SEQRES 9 A 264 HIS LEU LEU VAL ARG ILE GLY PRO ASN SER PHE SER ASP SEQRES 10 A 264 PRO GLN MET ILE ASP THR ILE ARG GLU GLN LEU ALA VAL SEQRES 11 A 264 TYR GLY VAL PRO GLY GLU ARG LEU TRP LEU GLN THR PRO SEQRES 12 A 264 GLU SER LYS VAL PHE THR HIS LEU ARG ASN ALA GLN GLN SEQRES 13 A 264 PHE LEU ALA ALA VAL SER ALA MET ASP CYS LYS VAL GLY SEQRES 14 A 264 LEU GLU GLN PHE GLY SER GLY LEU ASP SER PHE GLN LEU SEQRES 15 A 264 LEU ALA HIS PHE HIS PRO ALA PHE LEU LYS LEU ASP ARG SEQRES 16 A 264 GLY ILE THR GLY ASP ILE ALA SER ALA ARG ASP SER GLN SEQRES 17 A 264 GLU LYS ILE ARG GLU ILE THR SER ARG ALA GLN PRO ALA SEQRES 18 A 264 GLY ILE LEU THR MET ALA GLU PHE VAL ALA ASP ALA GLN SEQRES 19 A 264 SER MET SER SER PHE PHE SER ALA GLY VAL ASP TYR VAL SEQRES 20 A 264 GLN GLY ASP PHE VAL ALA PRO THR GLY PRO LEU MET ASN SEQRES 21 A 264 TYR GLU PHE GLY SEQRES 1 B 264 VAL SER ILE TYR ASP PRO ALA ALA ALA ASP ARG ALA GLU SEQRES 2 B 264 GLU GLU ARG ILE GLU ARG TRP VAL GLU GLN LEU ARG GLU SEQRES 3 B 264 ALA LEU VAL GLY ASP GLY PHE LEU LEU HIS TYR GLN PRO SEQRES 4 B 264 VAL LEU ASN LEU GLN GLY GLU PRO LEU GLU LEU TYR GLN SEQRES 5 B 264 ALA PHE LEU ARG LEU GLU ARG ASN GLY GLU MET MET SER SEQRES 6 B 264 PRO ASN ALA PHE MET ALA ILE ALA GLU GLU HIS ASP LEU SEQRES 7 B 264 VAL THR GLU ILE ASP ARG TRP VAL VAL ALA ARG ALA ILE SEQRES 8 B 264 ARG GLN LEU GLY GLU ARG GLN ARG ALA GLY HIS LYS THR SEQRES 9 B 264 HIS LEU LEU VAL ARG ILE GLY PRO ASN SER PHE SER ASP SEQRES 10 B 264 PRO GLN MET ILE ASP THR ILE ARG GLU GLN LEU ALA VAL SEQRES 11 B 264 TYR GLY VAL PRO GLY GLU ARG LEU TRP LEU GLN THR PRO SEQRES 12 B 264 GLU SER LYS VAL PHE THR HIS LEU ARG ASN ALA GLN GLN SEQRES 13 B 264 PHE LEU ALA ALA VAL SER ALA MET ASP CYS LYS VAL GLY SEQRES 14 B 264 LEU GLU GLN PHE GLY SER GLY LEU ASP SER PHE GLN LEU SEQRES 15 B 264 LEU ALA HIS PHE HIS PRO ALA PHE LEU LYS LEU ASP ARG SEQRES 16 B 264 GLY ILE THR GLY ASP ILE ALA SER ALA ARG ASP SER GLN SEQRES 17 B 264 GLU LYS ILE ARG GLU ILE THR SER ARG ALA GLN PRO ALA SEQRES 18 B 264 GLY ILE LEU THR MET ALA GLU PHE VAL ALA ASP ALA GLN SEQRES 19 B 264 SER MET SER SER PHE PHE SER ALA GLY VAL ASP TYR VAL SEQRES 20 B 264 GLN GLY ASP PHE VAL ALA PRO THR GLY PRO LEU MET ASN SEQRES 21 B 264 TYR GLU PHE GLY SEQRES 1 D 117 MET SER ALA MET ASN ALA ARG GLN GLY ILE LEU SER LEU SEQRES 2 D 117 ALA LEU LYS ASP LYS PRO ALA LEU TYR SER ALA TYR MET SEQRES 3 D 117 PRO PHE VAL LYS GLY GLY GLY ILE PHE VAL PRO THR PRO SEQRES 4 D 117 LYS ARG TYR MET LEU GLY ASP GLU VAL PHE LEU LEU LEU SEQRES 5 D 117 THR LEU PRO ASP SER SER GLU ARG LEU PRO VAL ALA GLY SEQRES 6 D 117 LYS VAL ILE TRP THR THR PRO ALA GLY ALA GLN GLY ASN SEQRES 7 D 117 ARG ALA ALA GLY ILE GLY VAL GLN PHE PRO ASP GLY PRO SEQRES 8 D 117 GLU GLY GLU ALA VAL ARG ASN LYS ILE GLU THR LEU LEU SEQRES 9 D 117 ALA GLY LEU THR THR SER ASP LYS PRO THR HIS THR MET SEQRES 1 C 117 MET SER ALA MET ASN ALA ARG GLN GLY ILE LEU SER LEU SEQRES 2 C 117 ALA LEU LYS ASP LYS PRO ALA LEU TYR SER ALA TYR MET SEQRES 3 C 117 PRO PHE VAL LYS GLY GLY GLY ILE PHE VAL PRO THR PRO SEQRES 4 C 117 LYS ARG TYR MET LEU GLY ASP GLU VAL PHE LEU LEU LEU SEQRES 5 C 117 THR LEU PRO ASP SER SER GLU ARG LEU PRO VAL ALA GLY SEQRES 6 C 117 LYS VAL ILE TRP THR THR PRO ALA GLY ALA GLN GLY ASN SEQRES 7 C 117 ARG ALA ALA GLY ILE GLY VAL GLN PHE PRO ASP GLY PRO SEQRES 8 C 117 GLU GLY GLU ALA VAL ARG ASN LYS ILE GLU THR LEU LEU SEQRES 9 C 117 ALA GLY LEU THR THR SER ASP LYS PRO THR HIS THR MET HET C2E A 701 46 HET CA A 702 1 HET CA A 703 1 HET C2E B 701 46 HET GOL B 702 6 HET GOL B 703 6 HET GOL B 704 6 HET CA B 705 1 HETNAM C2E 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10, HETNAM 2 C2E 12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3, HETNAM 3 C2E 2-D:3',2'-J][1,3,7,9,2, HETNAM 4 C2E 8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO- HETNAM 5 C2E 1,9-DIHYDRO-6H-PURIN-6-ONE) HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 C2E 2(C20 H24 N10 O14 P2) FORMUL 6 CA 3(CA 2+) FORMUL 9 GOL 3(C3 H8 O3) FORMUL 13 HOH *363(H2 O) HELIX 1 1 ASP A 430 LEU A 453 1 24 HELIX 2 2 SER A 490 HIS A 501 1 12 HELIX 3 3 LEU A 503 ALA A 525 1 23 HELIX 4 4 GLY A 536 PHE A 540 5 5 HELIX 5 5 ASP A 542 TYR A 556 1 15 HELIX 6 6 PRO A 559 GLU A 561 5 3 HELIX 7 7 GLU A 569 HIS A 575 1 7 HELIX 8 8 HIS A 575 ALA A 588 1 14 HELIX 9 9 ASP A 603 HIS A 610 5 8 HELIX 10 10 ASP A 619 GLY A 624 1 6 HELIX 11 11 ALA A 629 GLN A 644 1 16 HELIX 12 12 PRO A 645 GLY A 647 5 3 HELIX 13 13 ASP A 657 GLY A 668 1 12 HELIX 14 14 ASP B 430 GLY B 455 1 26 HELIX 15 15 SER B 490 HIS B 501 1 12 HELIX 16 16 LEU B 503 ALA B 525 1 23 HELIX 17 17 GLY B 536 SER B 541 5 6 HELIX 18 18 ASP B 542 GLY B 557 1 16 HELIX 19 19 PRO B 559 GLU B 561 5 3 HELIX 20 20 GLU B 569 HIS B 575 1 7 HELIX 21 21 HIS B 575 ALA B 588 1 14 HELIX 22 22 ASP B 603 ALA B 609 1 7 HELIX 23 23 ASP B 619 GLY B 624 1 6 HELIX 24 24 ALA B 629 GLN B 644 1 16 HELIX 25 25 ASP B 657 ALA B 667 1 11 HELIX 26 26 ASP D 17 ALA D 24 1 8 HELIX 27 27 GLY D 90 GLY D 106 1 17 HELIX 28 28 ASP C 17 ALA C 24 1 8 HELIX 29 29 GLY C 90 ALA C 105 1 16 SHEET 1 A 6 PHE A 458 PRO A 464 0 SHEET 2 A 6 GLU A 474 ARG A 484 -1 O PHE A 479 N HIS A 461 SHEET 3 A 6 GLU A 487 MET A 489 -1 O MET A 489 N LEU A 482 SHEET 4 A 6 ARG C 60 THR C 71 -1 O THR C 70 N MET A 488 SHEET 5 A 6 GLU C 47 THR C 53 -1 N LEU C 50 O VAL C 63 SHEET 6 A 6 LEU C 11 ALA C 14 1 N LEU C 13 O THR C 53 SHEET 1 B13 LEU A 466 ASN A 467 0 SHEET 2 B13 TYR A 671 VAL A 672 -1 O VAL A 672 N LEU A 466 SHEET 3 B13 LEU A 649 ALA A 652 1 N ALA A 652 O TYR A 671 SHEET 4 B13 PHE A 615 LEU A 618 1 N LEU A 618 O MET A 651 SHEET 5 B13 LYS A 592 PHE A 598 1 N LEU A 595 O LYS A 617 SHEET 6 B13 LEU A 563 PRO A 568 1 N LEU A 565 O LYS A 592 SHEET 7 B13 THR A 529 ARG A 534 1 N LEU A 531 O TRP A 564 SHEET 8 B13 GLU A 474 ARG A 484 1 N GLU A 474 O HIS A 530 SHEET 9 B13 GLU A 487 MET A 489 -1 O MET A 489 N LEU A 482 SHEET 10 B13 ARG C 60 THR C 71 -1 O THR C 70 N MET A 488 SHEET 11 B13 GLY C 82 GLN C 86 -1 O GLN C 86 N LYS C 66 SHEET 12 B13 GLY C 33 PRO C 37 -1 N VAL C 36 O ILE C 83 SHEET 13 B13 TYR C 25 MET C 26 -1 N MET C 26 O GLY C 33 SHEET 1 C 6 PHE B 458 PRO B 464 0 SHEET 2 C 6 LEU B 475 ARG B 484 -1 O GLN B 477 N GLN B 463 SHEET 3 C 6 GLU B 487 MET B 489 -1 O GLU B 487 N ARG B 484 SHEET 4 C 6 ARG D 60 THR D 71 -1 O THR D 70 N MET B 488 SHEET 5 C 6 GLU D 47 THR D 53 -1 N LEU D 52 O LEU D 61 SHEET 6 C 6 LEU D 11 ALA D 14 1 N LEU D 13 O THR D 53 SHEET 1 D13 LEU B 466 ASN B 467 0 SHEET 2 D13 TYR B 671 VAL B 672 -1 O VAL B 672 N LEU B 466 SHEET 3 D13 LEU B 649 ALA B 652 1 N ALA B 652 O TYR B 671 SHEET 4 D13 PHE B 615 LEU B 618 1 N LEU B 618 O MET B 651 SHEET 5 D13 LYS B 592 PHE B 598 1 N LEU B 595 O LYS B 617 SHEET 6 D13 LEU B 563 PRO B 568 1 N LEU B 565 O LYS B 592 SHEET 7 D13 HIS B 530 ARG B 534 1 N LEU B 531 O TRP B 564 SHEET 8 D13 LEU B 475 ARG B 484 1 N ALA B 478 O LEU B 532 SHEET 9 D13 GLU B 487 MET B 489 -1 O GLU B 487 N ARG B 484 SHEET 10 D13 ARG D 60 THR D 71 -1 O THR D 70 N MET B 488 SHEET 11 D13 GLY D 82 GLN D 86 -1 O GLY D 84 N ILE D 68 SHEET 12 D13 GLY D 33 PRO D 37 -1 N VAL D 36 O ILE D 83 SHEET 13 D13 TYR D 25 MET D 26 -1 N MET D 26 O GLY D 33 LINK OD1 ASP A 435 CA CA A 703 1555 1555 2.38 LINK O ASP A 502 CA CA A 702 1555 1555 2.30 LINK OD2BASP A 502 CA CA A 702 1555 1555 2.44 LINK OE2 GLU A 506 CA CA A 702 1555 1555 2.52 LINK OE1 GLU A 506 CA CA A 702 1555 1555 2.79 LINK CA CA A 702 O HOH A 810 1555 1555 2.58 LINK CA CA A 702 O HOH A 939 1555 1555 2.50 LINK CA CA A 702 O HOH A 971 1555 1555 2.75 LINK CA CA A 703 O HOH A 948 1555 1555 2.02 LINK CA CA A 703 OE2 GLU B 440 1555 1555 2.62 LINK CA CA A 703 O HOH B 876 1555 1555 2.23 LINK CA CA A 703 O HOH B 877 1555 1555 2.80 LINK CA CA A 703 O HOH B 878 1555 1555 2.24 LINK O HOH A 938 CA CA B 705 1555 1555 2.50 LINK OE1 GLU B 440 CA CA B 705 1555 1555 2.57 LINK OE1 GLU B 443 CA CA B 705 1555 1555 2.34 LINK CA CA B 705 O HOH B 879 1555 1555 2.62 LINK CA CA B 705 O HOH B 880 1555 1555 2.40 LINK CA CA B 705 O HOH C 225 1555 1555 2.52 LINK CA CA B 705 O HOH C 226 1555 1555 2.33 SITE 1 AC1 21 GLN A 463 ALA A 478 PHE A 479 LEU A 480 SITE 2 AC1 21 ARG A 481 SER A 490 PRO A 491 ASN A 492 SITE 3 AC1 21 ASP A 508 ARG A 534 GLU A 653 PHE A 654 SITE 4 AC1 21 GLN A 673 GLY A 674 HOH A 801 HOH A 838 SITE 5 AC1 21 HOH A 880 HOH A 887 HOH A 913 LEU C 44 SITE 6 AC1 21 HOH C 202 SITE 1 AC2 5 ASP A 502 GLU A 506 HOH A 810 HOH A 939 SITE 2 AC2 5 HOH A 971 SITE 1 AC3 6 ASP A 435 HOH A 948 GLU B 440 HOH B 876 SITE 2 AC3 6 HOH B 877 HOH B 878 SITE 1 AC4 20 GLN B 463 ALA B 478 PHE B 479 LEU B 480 SITE 2 AC4 20 ARG B 481 SER B 490 PRO B 491 ASN B 492 SITE 3 AC4 20 ASP B 508 ARG B 534 GLU B 653 PHE B 654 SITE 4 AC4 20 GLN B 673 GLY B 674 ASP B 675 HOH B 806 SITE 5 AC4 20 HOH B 821 HOH B 825 HOH B 844 HOH B 902 SITE 1 AC5 11 LEU B 553 ALA B 554 VAL B 558 PRO B 559 SITE 2 AC5 11 GLY B 560 MET B 589 GOL B 703 HOH B 801 SITE 3 AC5 11 HOH B 842 HOH B 859 HOH B 888 SITE 1 AC6 4 PRO A 543 GOL B 702 HOH B 892 HOH B 897 SITE 1 AC7 3 ARG B 522 MET B 684 HOH B 905 SITE 1 AC8 7 HOH A 938 GLU B 440 GLU B 443 HOH B 879 SITE 2 AC8 7 HOH B 880 HOH C 225 HOH C 226 CRYST1 126.787 126.787 107.317 90.00 90.00 120.00 P 65 12 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 0.007887 0.004554 0.000000 0.00000 SCALE2 0.000000 0.009107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009318 0.00000