HEADER TRANSCRIPTION 08-NOV-09 3KLO TITLE VIBRIO CHOLERAE VPST BOUND TO C-DI-GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR VPST; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 686; SOURCE 4 STRAIN: O1 EL TOR; SOURCE 5 GENE: VCA0952, VC_A0952; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS REC DOMAIN, HTH DOMAIN, DNA-BINDING, TRANSCRIPTION, TRANSCRIPTION KEYWDS 2 REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR P.V.KRASTEVA,V.A.S.NAVARRO,H.SONDERMANN REVDAT 3 06-SEP-23 3KLO 1 REMARK SEQADV HETSYN REVDAT 2 02-MAR-10 3KLO 1 JRNL REVDAT 1 09-FEB-10 3KLO 0 JRNL AUTH P.V.KRASTEVA,J.C.FONG,N.J.SHIKUMA,S.BEYHAN,M.V.NAVARRO, JRNL AUTH 2 F.H.YILDIZ,H.SONDERMANN JRNL TITL VIBRIO CHOLERAE VPST REGULATES MATRIX PRODUCTION AND JRNL TITL 2 MOTILITY BY DIRECTLY SENSING CYCLIC DI-GMP. JRNL REF SCIENCE V. 327 866 2010 JRNL REFN ISSN 0036-8075 JRNL PMID 20150502 JRNL DOI 10.1126/SCIENCE.1181185 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 2009_02_15_2320_3) 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.8 REMARK 3 NUMBER OF REFLECTIONS : 60780 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 3197 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 47.8691 - 7.9573 0.88 2657 146 0.2660 0.2582 REMARK 3 2 7.9573 - 6.3205 0.91 2747 152 0.2453 0.2793 REMARK 3 3 6.3205 - 5.5229 0.89 2693 143 0.2431 0.3097 REMARK 3 4 5.5229 - 5.0185 0.88 2683 145 0.2016 0.2811 REMARK 3 5 5.0185 - 4.6591 0.89 2655 156 0.1790 0.2034 REMARK 3 6 4.6591 - 4.3846 0.88 2655 143 0.1786 0.3023 REMARK 3 7 4.3846 - 4.1652 0.88 2676 149 0.2043 0.2601 REMARK 3 8 4.1652 - 3.9840 0.84 2526 140 0.1981 0.2239 REMARK 3 9 3.9840 - 3.8307 0.81 2447 130 0.2129 0.1913 REMARK 3 10 3.8307 - 3.6985 0.86 2614 140 0.2145 0.3292 REMARK 3 11 3.6985 - 3.5829 0.92 2785 152 0.2526 0.3287 REMARK 3 12 3.5829 - 3.4805 0.80 2421 129 0.2516 0.3288 REMARK 3 13 3.4805 - 3.3889 0.83 2507 152 0.2584 0.3282 REMARK 3 14 3.3889 - 3.3063 0.85 2574 138 0.2612 0.2876 REMARK 3 15 3.3063 - 3.2311 0.84 2535 138 0.2866 0.2851 REMARK 3 16 3.2311 - 3.1624 0.83 2514 138 0.2733 0.3176 REMARK 3 17 3.1624 - 3.0991 0.81 2422 135 0.2818 0.3058 REMARK 3 18 3.0991 - 3.0407 0.78 2369 137 0.2839 0.3278 REMARK 3 19 3.0407 - 2.9864 0.77 2288 138 0.2981 0.3001 REMARK 3 20 2.9864 - 2.9358 0.74 2252 125 0.3005 0.3864 REMARK 3 21 2.9358 - 2.8884 0.74 2250 121 0.3197 0.3265 REMARK 3 22 2.8884 - 2.8440 0.72 2173 127 0.3186 0.3830 REMARK 3 23 2.8440 - 2.8021 0.71 2140 123 0.3266 0.3782 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 27.91 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 2.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 0.007 6988 REMARK 3 ANGLE : 1.049 9471 REMARK 3 CHIRALITY : 0.073 1046 REMARK 3 PLANARITY : 0.011 1163 REMARK 3 DIHEDRAL : 20.482 2715 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 3KLO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056147. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0809 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60780 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 14.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3KLN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-CL, 0.8M POTASSIUM SODIUM REMARK 280 TARTRATE TETRAHYDRATE, 3-5% PEG-MME 5000, 8-12% XYLITOL, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 104.11350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 60.85150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 60.85150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.05675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 60.85150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 60.85150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 156.17025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 60.85150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.85150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 52.05675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 60.85150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.85150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 156.17025 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 104.11350 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: 1940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 -60.85150 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 60.85150 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 52.05675 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: 2450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 -60.85150 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 -60.85150 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -52.05675 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 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 GLU A 220 REMARK 465 GLU A 221 REMARK 465 VAL A 222 REMARK 465 ASN A 223 REMARK 465 SER A 224 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 ASP B 3 REMARK 465 GLU B 220 REMARK 465 GLU B 221 REMARK 465 VAL B 222 REMARK 465 ASN B 223 REMARK 465 SER B 224 REMARK 465 SER C 0 REMARK 465 MET C 1 REMARK 465 LYS C 2 REMARK 465 ASP C 3 REMARK 465 ILE C 217 REMARK 465 GLY C 218 REMARK 465 ILE C 219 REMARK 465 GLU C 220 REMARK 465 GLU C 221 REMARK 465 VAL C 222 REMARK 465 ASN C 223 REMARK 465 SER C 224 REMARK 465 SER D 0 REMARK 465 MET D 1 REMARK 465 LYS D 2 REMARK 465 ASP D 3 REMARK 465 SER D 153 REMARK 465 GLN D 154 REMARK 465 MET D 155 REMARK 465 TYR D 156 REMARK 465 ALA D 157 REMARK 465 LYS D 158 REMARK 465 LEU D 159 REMARK 465 THR D 160 REMARK 465 LYS D 161 REMARK 465 ARG D 162 REMARK 465 GLU D 163 REMARK 465 GLN D 164 REMARK 465 GLN D 165 REMARK 465 ILE D 166 REMARK 465 ILE D 167 REMARK 465 LYS D 168 REMARK 465 LEU D 169 REMARK 465 LEU D 170 REMARK 465 GLY D 171 REMARK 465 SER D 172 REMARK 465 GLY D 173 REMARK 465 ALA D 174 REMARK 465 SER D 175 REMARK 465 ASN D 176 REMARK 465 ILE D 177 REMARK 465 GLU D 178 REMARK 465 ILE D 179 REMARK 465 ALA D 180 REMARK 465 ASP D 181 REMARK 465 LYS D 182 REMARK 465 LEU D 183 REMARK 465 PHE D 184 REMARK 465 VAL D 185 REMARK 465 SER D 186 REMARK 465 GLU D 187 REMARK 465 ASN D 188 REMARK 465 THR D 189 REMARK 465 VAL D 190 REMARK 465 LYS D 191 REMARK 465 THR D 192 REMARK 465 ILE D 217 REMARK 465 GLY D 218 REMARK 465 ILE D 219 REMARK 465 GLU D 220 REMARK 465 GLU D 221 REMARK 465 VAL D 222 REMARK 465 ASN D 223 REMARK 465 SER D 224 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 ASP A 93 39.08 -91.80 REMARK 500 HIS A 143 -74.20 -51.56 REMARK 500 SER A 149 -103.22 -122.46 REMARK 500 SER A 153 -172.63 -68.54 REMARK 500 PHE A 198 19.12 -64.75 REMARK 500 ASN A 202 28.49 83.02 REMARK 500 ASN B 5 -26.33 70.02 REMARK 500 CYS B 80 59.13 -148.19 REMARK 500 TRP B 131 71.81 -118.60 REMARK 500 HIS B 143 -70.73 -62.83 REMARK 500 SER B 149 -125.68 -128.07 REMARK 500 ASN B 202 28.67 87.78 REMARK 500 CYS C 16 169.30 174.61 REMARK 500 TRP C 131 57.63 -112.90 REMARK 500 HIS C 143 -70.39 -52.42 REMARK 500 SER C 149 -53.33 -122.73 REMARK 500 THR C 160 -179.80 -63.53 REMARK 500 ASN C 202 18.61 85.60 REMARK 500 LYS D 6 116.70 -163.20 REMARK 500 CYS D 16 177.65 176.97 REMARK 500 ASN D 47 57.42 -114.77 REMARK 500 ASP D 128 15.38 80.30 REMARK 500 SER D 149 -90.28 -137.52 REMARK 500 LYS D 200 56.99 -90.11 REMARK 500 ASN D 205 -167.88 -162.33 REMARK 500 REMARK 500 REMARK: NULL 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 225 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E B 225 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAR B 226 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E C 225 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E D 225 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAR D 226 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KLN RELATED DB: PDB REMARK 900 EFFECTOR (APO-FORM) DBREF 3KLO A 1 224 UNP Q9KKZ8 Q9KKZ8_VIBCH 1 224 DBREF 3KLO B 1 224 UNP Q9KKZ8 Q9KKZ8_VIBCH 1 224 DBREF 3KLO C 1 224 UNP Q9KKZ8 Q9KKZ8_VIBCH 1 224 DBREF 3KLO D 1 224 UNP Q9KKZ8 Q9KKZ8_VIBCH 1 224 SEQADV 3KLO SER A 0 UNP Q9KKZ8 EXPRESSION TAG SEQADV 3KLO SER B 0 UNP Q9KKZ8 EXPRESSION TAG SEQADV 3KLO SER C 0 UNP Q9KKZ8 EXPRESSION TAG SEQADV 3KLO SER D 0 UNP Q9KKZ8 EXPRESSION TAG SEQRES 1 A 225 SER MET LYS ASP GLU ASN LYS LEU ASN VAL ARG MET LEU SEQRES 2 A 225 SER ASP VAL CYS MET GLN SER ARG LEU LEU LYS GLU ALA SEQRES 3 A 225 LEU GLU SER LYS LEU PRO LEU ALA LEU GLU ILE THR PRO SEQRES 4 A 225 PHE SER GLU LEU TRP LEU GLU GLU ASN LYS PRO GLU SER SEQRES 5 A 225 ARG SER ILE GLN MET LEU VAL ILE ASP TYR SER ARG ILE SEQRES 6 A 225 SER ASP ASP VAL LEU THR ASP TYR SER SER PHE LYS HIS SEQRES 7 A 225 ILE SER CYS PRO ASP ALA LYS GLU VAL ILE ILE ASN CYS SEQRES 8 A 225 PRO GLN ASP ILE GLU HIS LYS LEU LEU PHE LYS TRP ASN SEQRES 9 A 225 ASN LEU ALA GLY VAL PHE TYR ILE ASP ASP ASP MET ASP SEQRES 10 A 225 THR LEU ILE LYS GLY MET SER LYS ILE LEU GLN ASP GLU SEQRES 11 A 225 MET TRP LEU THR ARG LYS LEU ALA GLN GLU TYR ILE LEU SEQRES 12 A 225 HIS TYR ARG ALA GLY ASN SER VAL VAL THR SER GLN MET SEQRES 13 A 225 TYR ALA LYS LEU THR LYS ARG GLU GLN GLN ILE ILE LYS SEQRES 14 A 225 LEU LEU GLY SER GLY ALA SER ASN ILE GLU ILE ALA ASP SEQRES 15 A 225 LYS LEU PHE VAL SER GLU ASN THR VAL LYS THR HIS LEU SEQRES 16 A 225 HIS ASN VAL PHE LYS LYS ILE ASN ALA LYS ASN ARG LEU SEQRES 17 A 225 GLN ALA LEU ILE TRP ALA LYS ASN ASN ILE GLY ILE GLU SEQRES 18 A 225 GLU VAL ASN SER SEQRES 1 B 225 SER MET LYS ASP GLU ASN LYS LEU ASN VAL ARG MET LEU SEQRES 2 B 225 SER ASP VAL CYS MET GLN SER ARG LEU LEU LYS GLU ALA SEQRES 3 B 225 LEU GLU SER LYS LEU PRO LEU ALA LEU GLU ILE THR PRO SEQRES 4 B 225 PHE SER GLU LEU TRP LEU GLU GLU ASN LYS PRO GLU SER SEQRES 5 B 225 ARG SER ILE GLN MET LEU VAL ILE ASP TYR SER ARG ILE SEQRES 6 B 225 SER ASP ASP VAL LEU THR ASP TYR SER SER PHE LYS HIS SEQRES 7 B 225 ILE SER CYS PRO ASP ALA LYS GLU VAL ILE ILE ASN CYS SEQRES 8 B 225 PRO GLN ASP ILE GLU HIS LYS LEU LEU PHE LYS TRP ASN SEQRES 9 B 225 ASN LEU ALA GLY VAL PHE TYR ILE ASP ASP ASP MET ASP SEQRES 10 B 225 THR LEU ILE LYS GLY MET SER LYS ILE LEU GLN ASP GLU SEQRES 11 B 225 MET TRP LEU THR ARG LYS LEU ALA GLN GLU TYR ILE LEU SEQRES 12 B 225 HIS TYR ARG ALA GLY ASN SER VAL VAL THR SER GLN MET SEQRES 13 B 225 TYR ALA LYS LEU THR LYS ARG GLU GLN GLN ILE ILE LYS SEQRES 14 B 225 LEU LEU GLY SER GLY ALA SER ASN ILE GLU ILE ALA ASP SEQRES 15 B 225 LYS LEU PHE VAL SER GLU ASN THR VAL LYS THR HIS LEU SEQRES 16 B 225 HIS ASN VAL PHE LYS LYS ILE ASN ALA LYS ASN ARG LEU SEQRES 17 B 225 GLN ALA LEU ILE TRP ALA LYS ASN ASN ILE GLY ILE GLU SEQRES 18 B 225 GLU VAL ASN SER SEQRES 1 C 225 SER MET LYS ASP GLU ASN LYS LEU ASN VAL ARG MET LEU SEQRES 2 C 225 SER ASP VAL CYS MET GLN SER ARG LEU LEU LYS GLU ALA SEQRES 3 C 225 LEU GLU SER LYS LEU PRO LEU ALA LEU GLU ILE THR PRO SEQRES 4 C 225 PHE SER GLU LEU TRP LEU GLU GLU ASN LYS PRO GLU SER SEQRES 5 C 225 ARG SER ILE GLN MET LEU VAL ILE ASP TYR SER ARG ILE SEQRES 6 C 225 SER ASP ASP VAL LEU THR ASP TYR SER SER PHE LYS HIS SEQRES 7 C 225 ILE SER CYS PRO ASP ALA LYS GLU VAL ILE ILE ASN CYS SEQRES 8 C 225 PRO GLN ASP ILE GLU HIS LYS LEU LEU PHE LYS TRP ASN SEQRES 9 C 225 ASN LEU ALA GLY VAL PHE TYR ILE ASP ASP ASP MET ASP SEQRES 10 C 225 THR LEU ILE LYS GLY MET SER LYS ILE LEU GLN ASP GLU SEQRES 11 C 225 MET TRP LEU THR ARG LYS LEU ALA GLN GLU TYR ILE LEU SEQRES 12 C 225 HIS TYR ARG ALA GLY ASN SER VAL VAL THR SER GLN MET SEQRES 13 C 225 TYR ALA LYS LEU THR LYS ARG GLU GLN GLN ILE ILE LYS SEQRES 14 C 225 LEU LEU GLY SER GLY ALA SER ASN ILE GLU ILE ALA ASP SEQRES 15 C 225 LYS LEU PHE VAL SER GLU ASN THR VAL LYS THR HIS LEU SEQRES 16 C 225 HIS ASN VAL PHE LYS LYS ILE ASN ALA LYS ASN ARG LEU SEQRES 17 C 225 GLN ALA LEU ILE TRP ALA LYS ASN ASN ILE GLY ILE GLU SEQRES 18 C 225 GLU VAL ASN SER SEQRES 1 D 225 SER MET LYS ASP GLU ASN LYS LEU ASN VAL ARG MET LEU SEQRES 2 D 225 SER ASP VAL CYS MET GLN SER ARG LEU LEU LYS GLU ALA SEQRES 3 D 225 LEU GLU SER LYS LEU PRO LEU ALA LEU GLU ILE THR PRO SEQRES 4 D 225 PHE SER GLU LEU TRP LEU GLU GLU ASN LYS PRO GLU SER SEQRES 5 D 225 ARG SER ILE GLN MET LEU VAL ILE ASP TYR SER ARG ILE SEQRES 6 D 225 SER ASP ASP VAL LEU THR ASP TYR SER SER PHE LYS HIS SEQRES 7 D 225 ILE SER CYS PRO ASP ALA LYS GLU VAL ILE ILE ASN CYS SEQRES 8 D 225 PRO GLN ASP ILE GLU HIS LYS LEU LEU PHE LYS TRP ASN SEQRES 9 D 225 ASN LEU ALA GLY VAL PHE TYR ILE ASP ASP ASP MET ASP SEQRES 10 D 225 THR LEU ILE LYS GLY MET SER LYS ILE LEU GLN ASP GLU SEQRES 11 D 225 MET TRP LEU THR ARG LYS LEU ALA GLN GLU TYR ILE LEU SEQRES 12 D 225 HIS TYR ARG ALA GLY ASN SER VAL VAL THR SER GLN MET SEQRES 13 D 225 TYR ALA LYS LEU THR LYS ARG GLU GLN GLN ILE ILE LYS SEQRES 14 D 225 LEU LEU GLY SER GLY ALA SER ASN ILE GLU ILE ALA ASP SEQRES 15 D 225 LYS LEU PHE VAL SER GLU ASN THR VAL LYS THR HIS LEU SEQRES 16 D 225 HIS ASN VAL PHE LYS LYS ILE ASN ALA LYS ASN ARG LEU SEQRES 17 D 225 GLN ALA LEU ILE TRP ALA LYS ASN ASN ILE GLY ILE GLU SEQRES 18 D 225 GLU VAL ASN SER HET C2E A 225 46 HET C2E B 225 46 HET TAR B 226 10 HET C2E C 225 46 HET C2E D 225 46 HET TAR D 226 10 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 TAR D(-)-TARTARIC ACID HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 5 C2E 4(C20 H24 N10 O14 P2) FORMUL 7 TAR 2(C4 H6 O6) FORMUL 11 HOH *49(H2 O) HELIX 1 1 CYS A 16 LEU A 30 1 15 HELIX 2 2 PRO A 38 SER A 40 5 3 HELIX 3 3 GLU A 41 GLU A 46 1 6 HELIX 4 4 PRO A 49 ILE A 54 5 6 HELIX 5 5 SER A 62 ILE A 64 5 3 HELIX 6 6 SER A 65 CYS A 80 1 16 HELIX 7 7 GLU A 95 PHE A 100 1 6 HELIX 8 8 ASP A 114 GLN A 127 1 14 HELIX 9 9 THR A 133 ALA A 146 1 14 HELIX 10 10 SER A 153 LYS A 158 1 6 HELIX 11 11 THR A 160 GLY A 171 1 12 HELIX 12 12 SER A 175 LEU A 183 1 9 HELIX 13 13 SER A 186 PHE A 198 1 13 HELIX 14 14 ASN A 205 ILE A 217 1 13 HELIX 15 15 CYS B 16 LEU B 30 1 15 HELIX 16 16 PRO B 38 SER B 40 5 3 HELIX 17 17 GLU B 41 GLU B 46 1 6 HELIX 18 18 LYS B 48 ILE B 54 5 7 HELIX 19 19 SER B 62 ILE B 64 5 3 HELIX 20 20 SER B 65 ASP B 67 5 3 HELIX 21 21 VAL B 68 CYS B 80 1 13 HELIX 22 22 GLU B 95 PHE B 100 1 6 HELIX 23 23 ASP B 114 GLN B 127 1 14 HELIX 24 24 THR B 133 ALA B 146 1 14 HELIX 25 25 SER B 153 LEU B 159 1 7 HELIX 26 26 THR B 160 GLY B 171 1 12 HELIX 27 27 SER B 175 LEU B 183 1 9 HELIX 28 28 SER B 186 ASN B 202 1 17 HELIX 29 29 ASN B 205 ILE B 217 1 13 HELIX 30 30 CYS C 16 LEU C 30 1 15 HELIX 31 31 PRO C 38 SER C 40 5 3 HELIX 32 32 GLU C 41 GLU C 46 1 6 HELIX 33 33 LYS C 48 ILE C 54 5 7 HELIX 34 34 SER C 62 ILE C 64 5 3 HELIX 35 35 SER C 65 ASP C 67 5 3 HELIX 36 36 VAL C 68 CYS C 80 1 13 HELIX 37 37 GLU C 95 PHE C 100 1 6 HELIX 38 38 ASP C 114 GLN C 127 1 14 HELIX 39 39 THR C 133 GLY C 147 1 15 HELIX 40 40 SER C 153 LYS C 158 1 6 HELIX 41 41 THR C 160 GLY C 171 1 12 HELIX 42 42 SER C 175 LEU C 183 1 9 HELIX 43 43 SER C 186 PHE C 198 1 13 HELIX 44 44 ASN C 205 ASN C 216 1 12 HELIX 45 45 CYS D 16 LEU D 30 1 15 HELIX 46 46 GLU D 41 GLU D 45 5 5 HELIX 47 47 LYS D 48 ILE D 54 5 7 HELIX 48 48 SER D 62 ILE D 64 5 3 HELIX 49 49 ASP D 66 CYS D 80 1 15 HELIX 50 50 GLU D 95 TRP D 102 5 8 HELIX 51 51 ASP D 114 GLN D 127 1 14 HELIX 52 52 THR D 133 ALA D 146 1 14 HELIX 53 53 HIS D 195 LYS D 199 5 5 HELIX 54 54 ASN D 205 ASN D 215 1 11 SHEET 1 A 5 LEU A 32 THR A 37 0 SHEET 2 A 5 LEU A 7 LEU A 12 1 N LEU A 7 O ALA A 33 SHEET 3 A 5 MET A 56 ASP A 60 1 O MET A 56 N ARG A 10 SHEET 4 A 5 LYS A 84 CYS A 90 1 O VAL A 86 N ILE A 59 SHEET 5 A 5 LEU A 105 TYR A 110 1 O ALA A 106 N GLU A 85 SHEET 1 B 5 LEU B 32 THR B 37 0 SHEET 2 B 5 LEU B 7 LEU B 12 1 N LEU B 7 O ALA B 33 SHEET 3 B 5 MET B 56 ASP B 60 1 O MET B 56 N ARG B 10 SHEET 4 B 5 LYS B 84 CYS B 90 1 O VAL B 86 N LEU B 57 SHEET 5 B 5 LEU B 105 TYR B 110 1 O PHE B 109 N CYS B 90 SHEET 1 C 5 LEU C 32 THR C 37 0 SHEET 2 C 5 LEU C 7 LEU C 12 1 N LEU C 7 O ALA C 33 SHEET 3 C 5 MET C 56 ASP C 60 1 O VAL C 58 N LEU C 12 SHEET 4 C 5 LYS C 84 CYS C 90 1 O VAL C 86 N ILE C 59 SHEET 5 C 5 LEU C 105 TYR C 110 1 O ALA C 106 N GLU C 85 SHEET 1 D 5 LEU D 32 THR D 37 0 SHEET 2 D 5 LEU D 7 LEU D 12 1 N LEU D 7 O ALA D 33 SHEET 3 D 5 MET D 56 ASP D 60 1 O VAL D 58 N LEU D 12 SHEET 4 D 5 LYS D 84 CYS D 90 1 O LYS D 84 N LEU D 57 SHEET 5 D 5 LEU D 105 TYR D 110 1 O ALA D 106 N GLU D 85 CISPEP 1 LYS A 199 LYS A 200 0 10.78 CISPEP 2 GLY B 218 ILE B 219 0 1.75 CISPEP 3 LYS C 199 LYS C 200 0 6.34 CISPEP 4 LYS D 199 LYS D 200 0 0.75 SITE 1 AC1 8 LYS A 120 TRP A 131 THR A 133 ARG A 134 SITE 2 AC1 8 HOH A 235 ARG B 134 C2E B 225 TAR B 226 SITE 1 AC2 9 ARG A 134 C2E A 225 TRP B 131 THR B 133 SITE 2 AC2 9 ARG B 134 TAR B 226 HOH B 237 HOH B 238 SITE 3 AC2 9 HOH B 239 SITE 1 AC3 6 ARG A 134 LYS A 135 C2E A 225 LYS B 124 SITE 2 AC3 6 GLU B 129 C2E B 225 SITE 1 AC4 9 LYS C 120 MET C 130 TRP C 131 THR C 133 SITE 2 AC4 9 ARG C 134 HOH C 229 ARG D 134 C2E D 225 SITE 3 AC4 9 TAR D 226 SITE 1 AC5 8 ARG C 134 C2E C 225 LYS D 120 TRP D 131 SITE 2 AC5 8 THR D 133 ARG D 134 TAR D 226 HOH D 235 SITE 1 AC6 6 ARG C 134 LYS C 135 C2E C 225 LYS D 124 SITE 2 AC6 6 GLU D 129 C2E D 225 CRYST1 121.703 121.703 208.227 90.00 90.00 90.00 P 41 21 2 32 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 0.008217 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008217 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004802 0.00000