HEADER SIGNALING PROTEIN 23-JUL-19 6PWK TITLE VIBRIO CHOLERAE LAPD S HELIX-GGDEF-EAL (BOUND TO C-DI-GMP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GGDEF AND EAL DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE O1 STR. 2010EL-1786; SOURCE 3 ORGANISM_TAXID: 914149; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BIOFILM FORMATION, CELL ADHESION, C-DI-GMP SIGNALING, RECEPTOR, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.M.GIGLIO,R.B.COOLEY,H.SONDERMANN REVDAT 4 11-OCT-23 6PWK 1 LINK REVDAT 3 22-APR-20 6PWK 1 JRNL HETSYN REVDAT 2 27-NOV-19 6PWK 1 REMARK REVDAT 1 09-OCT-19 6PWK 0 JRNL AUTH G.KITTS,K.M.GIGLIO,D.ZAMORANO-SANCHEZ,J.H.PARK,L.TOWNSLEY, JRNL AUTH 2 R.B.COOLEY,B.R.WUCHER,K.E.KLOSE,C.D.NADELL,F.H.YILDIZ, JRNL AUTH 3 H.SONDERMANN JRNL TITL A CONSERVED REGULATORY CIRCUIT CONTROLS LARGE ADHESINS IN JRNL TITL 2 VIBRIO CHOLERAE. JRNL REF MBIO V. 10 2019 JRNL REFN ESSN 2150-7511 JRNL PMID 31796544 JRNL DOI 10.1128/MBIO.02822-19 REMARK 2 REMARK 2 RESOLUTION. 2.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 30983 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.450 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 33.7700 - 6.2700 1.00 2161 149 0.1602 0.2004 REMARK 3 2 6.2700 - 4.9800 1.00 2103 149 0.2023 0.2362 REMARK 3 3 4.9800 - 4.3600 1.00 2108 147 0.1647 0.2221 REMARK 3 4 4.3600 - 3.9600 1.00 2104 134 0.1730 0.2231 REMARK 3 5 3.9600 - 3.6700 1.00 2102 151 0.1914 0.2129 REMARK 3 6 3.6700 - 3.4600 1.00 2086 147 0.2049 0.2616 REMARK 3 7 3.4600 - 3.2900 1.00 2109 144 0.2255 0.3193 REMARK 3 8 3.2900 - 3.1400 1.00 2081 146 0.2514 0.3284 REMARK 3 9 3.1400 - 3.0200 1.00 2117 136 0.2527 0.3204 REMARK 3 10 3.0200 - 2.9200 1.00 2076 150 0.2395 0.3238 REMARK 3 11 2.9200 - 2.8300 1.00 2067 137 0.2596 0.3051 REMARK 3 12 2.8300 - 2.7500 1.00 2117 148 0.2635 0.3132 REMARK 3 13 2.7500 - 2.6700 1.00 2058 139 0.2794 0.3605 REMARK 3 14 2.6700 - 2.6100 0.81 1695 122 0.3110 0.3877 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.413 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.02 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 : 0.002 6765 REMARK 3 ANGLE : 0.662 9213 REMARK 3 CHIRALITY : 0.043 1027 REMARK 3 PLANARITY : 0.003 1159 REMARK 3 DIHEDRAL : 16.726 3898 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 222:401 REMARK 3 ORIGIN FOR THE GROUP (A): -36.9314 -0.9297 1.0421 REMARK 3 T TENSOR REMARK 3 T11: 0.6606 T22: 0.5903 REMARK 3 T33: 0.5888 T12: 0.1246 REMARK 3 T13: -0.0229 T23: 0.0826 REMARK 3 L TENSOR REMARK 3 L11: 4.5442 L22: 2.4923 REMARK 3 L33: 3.7985 L12: 1.3517 REMARK 3 L13: -1.4772 L23: -1.0075 REMARK 3 S TENSOR REMARK 3 S11: 0.0711 S12: -0.3821 S13: -0.5303 REMARK 3 S21: 0.1554 S22: -0.2512 S23: -0.1894 REMARK 3 S31: 0.4139 S32: 0.6316 S33: 0.1908 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 402:635 REMARK 3 ORIGIN FOR THE GROUP (A): -34.9169 10.4184 -29.1618 REMARK 3 T TENSOR REMARK 3 T11: 0.4389 T22: 0.5866 REMARK 3 T33: 0.4342 T12: 0.0509 REMARK 3 T13: 0.0112 T23: -0.0455 REMARK 3 L TENSOR REMARK 3 L11: 3.6103 L22: 2.3547 REMARK 3 L33: 2.3457 L12: 0.2995 REMARK 3 L13: -0.0490 L23: 0.6913 REMARK 3 S TENSOR REMARK 3 S11: -0.0157 S12: 0.7471 S13: -0.2052 REMARK 3 S21: -0.2888 S22: -0.0578 S23: 0.0156 REMARK 3 S31: 0.2927 S32: 0.1594 S33: 0.0713 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN B AND RESID 222:395 REMARK 3 ORIGIN FOR THE GROUP (A): -67.6067 12.1162 6.9132 REMARK 3 T TENSOR REMARK 3 T11: 0.6763 T22: 0.4959 REMARK 3 T33: 0.5176 T12: -0.0120 REMARK 3 T13: 0.0719 T23: 0.0272 REMARK 3 L TENSOR REMARK 3 L11: 6.2403 L22: 0.7768 REMARK 3 L33: 3.1059 L12: -0.5611 REMARK 3 L13: 1.4951 L23: 0.4898 REMARK 3 S TENSOR REMARK 3 S11: 0.0693 S12: -0.5531 S13: 0.3624 REMARK 3 S21: 0.1048 S22: -0.0209 S23: -0.1277 REMARK 3 S31: -0.2153 S32: -0.1650 S33: -0.0413 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND RESID 396:635 REMARK 3 ORIGIN FOR THE GROUP (A): -75.7595 14.1287 -24.3238 REMARK 3 T TENSOR REMARK 3 T11: 0.4172 T22: 0.5074 REMARK 3 T33: 0.4675 T12: -0.0554 REMARK 3 T13: -0.0292 T23: -0.0361 REMARK 3 L TENSOR REMARK 3 L11: 4.2615 L22: 2.3678 REMARK 3 L33: 1.8801 L12: -0.5869 REMARK 3 L13: 0.3893 L23: 0.0541 REMARK 3 S TENSOR REMARK 3 S11: -0.0098 S12: 0.5306 S13: -0.0196 REMARK 3 S21: -0.1001 S22: -0.0182 S23: -0.0308 REMARK 3 S31: 0.0811 S32: -0.0098 S33: 0.0130 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 6PWK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000243200. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31030 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 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: PHENIX REMARK 200 STARTING MODEL: 3PJX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FORMATE, 0.1M BICINE, PH REMARK 280 8.5; 20% W/V PEG MME 5000, AND 0.5-1 MM C-DI-GMP, 20% XYLITOL, 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 45.11050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 LYS A 221 REMARK 465 ASP A 346 REMARK 465 PRO A 347 REMARK 465 THR A 348 REMARK 465 GLY A 349 REMARK 465 MET A 350 REMARK 465 ALA A 351 REMARK 465 LYS A 352 REMARK 465 ALA A 353 REMARK 465 LYS A 636 REMARK 465 ALA A 637 REMARK 465 ALA A 638 REMARK 465 LYS B 221 REMARK 465 PRO B 345 REMARK 465 ASP B 346 REMARK 465 PRO B 347 REMARK 465 THR B 348 REMARK 465 GLY B 349 REMARK 465 MET B 350 REMARK 465 ALA B 351 REMARK 465 LYS B 352 REMARK 465 ALA B 353 REMARK 465 LYS B 636 REMARK 465 ALA B 637 REMARK 465 ALA B 638 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 224 CG CD CE NZ REMARK 470 GLU A 484 CG CD OE1 OE2 REMARK 470 PHE A 560 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 561 CG CD OE1 NE2 REMARK 470 SER A 562 OG REMARK 470 LEU A 563 CG CD1 CD2 REMARK 470 ASP A 585 CG OD1 OD2 REMARK 470 ASP A 586 CG OD1 OD2 REMARK 470 GLU A 587 CG CD OE1 OE2 REMARK 470 ARG A 588 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 589 CG CD OE1 NE2 REMARK 470 LYS A 590 CG CD CE NZ REMARK 470 PHE A 591 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 224 CG CD CE NZ REMARK 470 PHE B 560 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 561 CG CD OE1 NE2 REMARK 470 SER B 562 OG REMARK 470 LEU B 563 CG CD1 CD2 REMARK 470 ARG B 588 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 589 CG CD OE1 NE2 REMARK 470 LYS B 590 CG CD CE NZ 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 SER A 262 -52.54 -124.12 REMARK 500 ASN A 555 44.61 -97.19 REMARK 500 ASN A 559 64.60 -102.46 REMARK 500 GLN A 561 -1.04 60.85 REMARK 500 PHE A 625 57.01 39.48 REMARK 500 SER B 262 -56.26 -123.88 REMARK 500 ASP B 446 59.83 31.85 REMARK 500 ASN B 559 71.67 -107.90 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 MG A 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 438 OE2 REMARK 620 2 ASN A 492 OD1 79.7 REMARK 620 3 GLU A 524 OE1 72.8 93.0 REMARK 620 4 ASP A 554 OD1 142.8 131.0 83.8 REMARK 620 5 ASP A 554 OD2 159.8 80.1 108.7 55.6 REMARK 620 6 C2E A 701 O2P 95.3 97.0 162.9 99.9 86.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 438 OE2 REMARK 620 2 ASN B 492 OD1 93.5 REMARK 620 3 GLU B 524 OE1 84.8 100.6 REMARK 620 4 ASP B 554 OD2 174.7 89.9 90.5 REMARK 620 5 C2E B 701 O2P 91.9 102.0 157.3 91.4 REMARK 620 6 HOH B 804 O 91.8 173.2 84.1 85.2 73.5 REMARK 620 N 1 2 3 4 5 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 C2E A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG 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 C2E B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 703 DBREF1 6PWK A 221 636 UNP A0A0H6T0A6_VIBCL DBREF2 6PWK A A0A0H6T0A6 119 534 DBREF1 6PWK B 221 636 UNP A0A0H6T0A6_VIBCL DBREF2 6PWK B A0A0H6T0A6 119 534 SEQADV 6PWK ALA A 637 UNP A0A0H6T0A EXPRESSION TAG SEQADV 6PWK ALA A 638 UNP A0A0H6T0A EXPRESSION TAG SEQADV 6PWK ALA B 637 UNP A0A0H6T0A EXPRESSION TAG SEQADV 6PWK ALA B 638 UNP A0A0H6T0A EXPRESSION TAG SEQRES 1 A 418 LYS ALA PHE LYS ALA GLN ALA LYS GLU ALA GLN GLN LEU SEQRES 2 A 418 ARG GLU ARG ALA TYR LEU ASP PRO VAL SER HIS LEU GLY SEQRES 3 A 418 ASN ARG ALA TYR TYR MET SER GLN LEU SER GLY TRP LEU SEQRES 4 A 418 SER GLU SER GLY ILE GLY GLY VAL ALA ILE LEU GLN ALA SEQRES 5 A 418 GLU PHE ILE LYS GLU LEU TYR GLU GLU LYS GLY TYR GLU SEQRES 6 A 418 ALA GLY ASP GLY MET VAL ARG GLU LEU ALA ASP ARG LEU SEQRES 7 A 418 LYS ASN SER ILE THR ILE LYS ASP ILE SER ILE ALA ARG SEQRES 8 A 418 ILE SER THR TYR GLU PHE GLY ILE ILE MET PRO ASN MET SEQRES 9 A 418 ASP GLU THR GLU LEU LYS ILE VAL ALA GLU SER ILE ILE SEQRES 10 A 418 THR CYS VAL ASP ASP ILE ASN PRO ASP PRO THR GLY MET SEQRES 11 A 418 ALA LYS ALA ASN LEU SER LEU GLY VAL VAL SER ASN LYS SEQRES 12 A 418 ARG GLN SER SER THR THR THR LEU LEU SER LEU LEU ASP SEQRES 13 A 418 ASN ALA LEU ALA LYS ALA LYS SER ASN PRO GLU LEU ASN SEQRES 14 A 418 TYR GLY PHE ILE SER SER ASP THR ASP LYS ILE ILE LEU SEQRES 15 A 418 GLY LYS GLN GLN TRP LYS THR LEU VAL GLU GLU ALA ILE SEQRES 16 A 418 HIS ASN ASP TRP PHE THR PHE ARG TYR GLN ALA ALA ASN SEQRES 17 A 418 SER SER TRP GLY LYS THR PHE HIS ARG GLU VAL PHE SER SEQRES 18 A 418 ALA PHE GLU LYS ASP GLY VAL ARG TYR THR ALA ASN GLN SEQRES 19 A 418 PHE LEU PHE ALA LEU GLU GLN LEU ASN ALA SER HIS ILE SEQRES 20 A 418 PHE ASP GLN TYR VAL ILE GLU ARG VAL ILE GLN GLN LEU SEQRES 21 A 418 GLU LYS GLY GLU LEU THR ASP PRO LEU ALA ILE ASN ILE SEQRES 22 A 418 ALA GLN GLY SER ILE SER GLN PRO SER PHE ILE ARG TRP SEQRES 23 A 418 ILE SER GLN THR LEU SER LYS HIS LEU SER VAL ALA ASN SEQRES 24 A 418 LEU LEU HIS PHE GLU ILE PRO GLU GLY CYS PHE VAL ASN SEQRES 25 A 418 GLU PRO HIS TYR THR ALA LEU PHE CYS ASN ALA VAL ARG SEQRES 26 A 418 ASN ALA GLY ALA ASP PHE GLY VAL ASP ASN TYR GLY ARG SEQRES 27 A 418 ASN PHE GLN SER LEU ASP TYR ILE ASN GLU PHE ARG PRO SEQRES 28 A 418 LYS TYR VAL LYS LEU ASP TYR LEU PHE THR HIS HIS LEU SEQRES 29 A 418 ASP ASP GLU ARG GLN LYS PHE THR LEU THR SER ILE SER SEQRES 30 A 418 ARG THR ALA HIS ASN LEU GLY ILE THR THR ILE ALA SER SEQRES 31 A 418 ARG VAL GLU THR GLN THR GLN LEU ASP PHE LEU SER GLU SEQRES 32 A 418 HIS PHE ILE GLU VAL PHE GLN GLY PHE ILE VAL ASP LYS SEQRES 33 A 418 ALA ALA SEQRES 1 B 418 LYS ALA PHE LYS ALA GLN ALA LYS GLU ALA GLN GLN LEU SEQRES 2 B 418 ARG GLU ARG ALA TYR LEU ASP PRO VAL SER HIS LEU GLY SEQRES 3 B 418 ASN ARG ALA TYR TYR MET SER GLN LEU SER GLY TRP LEU SEQRES 4 B 418 SER GLU SER GLY ILE GLY GLY VAL ALA ILE LEU GLN ALA SEQRES 5 B 418 GLU PHE ILE LYS GLU LEU TYR GLU GLU LYS GLY TYR GLU SEQRES 6 B 418 ALA GLY ASP GLY MET VAL ARG GLU LEU ALA ASP ARG LEU SEQRES 7 B 418 LYS ASN SER ILE THR ILE LYS ASP ILE SER ILE ALA ARG SEQRES 8 B 418 ILE SER THR TYR GLU PHE GLY ILE ILE MET PRO ASN MET SEQRES 9 B 418 ASP GLU THR GLU LEU LYS ILE VAL ALA GLU SER ILE ILE SEQRES 10 B 418 THR CYS VAL ASP ASP ILE ASN PRO ASP PRO THR GLY MET SEQRES 11 B 418 ALA LYS ALA ASN LEU SER LEU GLY VAL VAL SER ASN LYS SEQRES 12 B 418 ARG GLN SER SER THR THR THR LEU LEU SER LEU LEU ASP SEQRES 13 B 418 ASN ALA LEU ALA LYS ALA LYS SER ASN PRO GLU LEU ASN SEQRES 14 B 418 TYR GLY PHE ILE SER SER ASP THR ASP LYS ILE ILE LEU SEQRES 15 B 418 GLY LYS GLN GLN TRP LYS THR LEU VAL GLU GLU ALA ILE SEQRES 16 B 418 HIS ASN ASP TRP PHE THR PHE ARG TYR GLN ALA ALA ASN SEQRES 17 B 418 SER SER TRP GLY LYS THR PHE HIS ARG GLU VAL PHE SER SEQRES 18 B 418 ALA PHE GLU LYS ASP GLY VAL ARG TYR THR ALA ASN GLN SEQRES 19 B 418 PHE LEU PHE ALA LEU GLU GLN LEU ASN ALA SER HIS ILE SEQRES 20 B 418 PHE ASP GLN TYR VAL ILE GLU ARG VAL ILE GLN GLN LEU SEQRES 21 B 418 GLU LYS GLY GLU LEU THR ASP PRO LEU ALA ILE ASN ILE SEQRES 22 B 418 ALA GLN GLY SER ILE SER GLN PRO SER PHE ILE ARG TRP SEQRES 23 B 418 ILE SER GLN THR LEU SER LYS HIS LEU SER VAL ALA ASN SEQRES 24 B 418 LEU LEU HIS PHE GLU ILE PRO GLU GLY CYS PHE VAL ASN SEQRES 25 B 418 GLU PRO HIS TYR THR ALA LEU PHE CYS ASN ALA VAL ARG SEQRES 26 B 418 ASN ALA GLY ALA ASP PHE GLY VAL ASP ASN TYR GLY ARG SEQRES 27 B 418 ASN PHE GLN SER LEU ASP TYR ILE ASN GLU PHE ARG PRO SEQRES 28 B 418 LYS TYR VAL LYS LEU ASP TYR LEU PHE THR HIS HIS LEU SEQRES 29 B 418 ASP ASP GLU ARG GLN LYS PHE THR LEU THR SER ILE SER SEQRES 30 B 418 ARG THR ALA HIS ASN LEU GLY ILE THR THR ILE ALA SER SEQRES 31 B 418 ARG VAL GLU THR GLN THR GLN LEU ASP PHE LEU SER GLU SEQRES 32 B 418 HIS PHE ILE GLU VAL PHE GLN GLY PHE ILE VAL ASP LYS SEQRES 33 B 418 ALA ALA HET C2E A 701 46 HET C2E A 702 46 HET MG A 703 1 HET C2E B 701 46 HET C2E B 702 46 HET MG B 703 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 MG MAGNESIUM ION HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 3 C2E 4(C20 H24 N10 O14 P2) FORMUL 5 MG 2(MG 2+) FORMUL 9 HOH *40(H2 O) HELIX 1 AA1 ALA A 222 LEU A 239 1 18 HELIX 2 AA2 ASN A 247 SER A 262 1 16 HELIX 3 AA3 ALA A 272 SER A 301 1 30 HELIX 4 AA4 ASP A 325 CYS A 339 1 15 HELIX 5 AA5 SER A 367 ASN A 385 1 19 HELIX 6 AA6 GLY A 403 ASP A 418 1 16 HELIX 7 AA7 ALA A 452 LEU A 462 1 11 HELIX 8 AA8 ALA A 464 LYS A 482 1 19 HELIX 9 AA9 ALA A 494 SER A 499 1 6 HELIX 10 AB1 GLN A 500 LYS A 513 1 14 HELIX 11 AB2 HIS A 514 ASN A 519 5 6 HELIX 12 AB3 PRO A 526 GLU A 533 1 8 HELIX 13 AB4 GLU A 533 ALA A 547 1 15 HELIX 14 AB5 ASP A 564 ARG A 570 1 7 HELIX 15 AB6 TYR A 578 HIS A 582 5 5 HELIX 16 AB7 ASP A 586 LEU A 603 1 18 HELIX 17 AB8 THR A 614 GLU A 623 1 10 HELIX 18 AB9 PHE B 223 LEU B 239 1 17 HELIX 19 AC1 ASN B 247 SER B 262 1 16 HELIX 20 AC2 ALA B 272 ILE B 302 1 31 HELIX 21 AC3 ASP B 325 ASP B 342 1 18 HELIX 22 AC4 SER B 367 ASN B 385 1 19 HELIX 23 AC5 GLY B 403 ASP B 418 1 16 HELIX 24 AC6 ALA B 452 GLN B 461 1 10 HELIX 25 AC7 ALA B 464 LYS B 482 1 19 HELIX 26 AC8 ALA B 494 SER B 499 1 6 HELIX 27 AC9 GLN B 500 LYS B 513 1 14 HELIX 28 AD1 HIS B 514 ASN B 519 5 6 HELIX 29 AD2 GLU B 527 GLU B 533 1 7 HELIX 30 AD3 GLU B 533 ALA B 547 1 15 HELIX 31 AD4 ASP B 564 ARG B 570 1 7 HELIX 32 AD5 TYR B 578 THR B 581 5 4 HELIX 33 AD6 ASP B 586 LEU B 603 1 18 HELIX 34 AD7 THR B 614 GLU B 623 1 10 SHEET 1 AA1 5 SER A 308 ALA A 310 0 SHEET 2 AA1 5 GLU A 316 PRO A 322 -1 O GLY A 318 N ALA A 310 SHEET 3 AA1 5 GLY A 265 GLN A 271 -1 N LEU A 270 O PHE A 317 SHEET 4 AA1 5 SER A 356 ASN A 362 -1 O VAL A 360 N VAL A 267 SHEET 5 AA1 5 GLY A 391 SER A 394 1 O GLY A 391 N VAL A 359 SHEET 1 AA210 VAL A 448 THR A 451 0 SHEET 2 AA210 THR A 434 LYS A 445 -1 N PHE A 443 O TYR A 450 SHEET 3 AA210 LEU A 489 ASN A 492 1 O ALA A 490 N VAL A 439 SHEET 4 AA210 LEU A 521 ILE A 525 1 O GLU A 524 N ILE A 491 SHEET 5 AA210 ASP A 550 TYR A 556 1 O GLY A 552 N ILE A 525 SHEET 6 AA210 TYR A 573 LEU A 576 1 O LYS A 575 N VAL A 553 SHEET 7 AA210 THR A 606 ALA A 609 1 O ILE A 608 N LEU A 576 SHEET 8 AA210 VAL A 628 PHE A 629 1 O VAL A 628 N ALA A 609 SHEET 9 AA210 PHE A 420 SER A 429 -1 N ASN A 428 O PHE A 629 SHEET 10 AA210 THR A 434 LYS A 445 -1 O ALA A 442 N THR A 421 SHEET 1 AA3 5 SER B 308 ALA B 310 0 SHEET 2 AA3 5 GLU B 316 PRO B 322 -1 O GLY B 318 N ALA B 310 SHEET 3 AA3 5 GLY B 265 GLN B 271 -1 N LEU B 270 O PHE B 317 SHEET 4 AA3 5 SER B 356 ASN B 362 -1 O GLY B 358 N ILE B 269 SHEET 5 AA3 5 GLY B 391 SER B 394 1 O GLY B 391 N VAL B 359 SHEET 1 AA410 VAL B 448 THR B 451 0 SHEET 2 AA410 THR B 434 LYS B 445 -1 N PHE B 443 O TYR B 450 SHEET 3 AA410 LEU B 489 ASN B 492 1 O ALA B 490 N VAL B 439 SHEET 4 AA410 LEU B 521 PRO B 526 1 O HIS B 522 N ILE B 491 SHEET 5 AA410 ASP B 550 TYR B 556 1 O ASP B 554 N ILE B 525 SHEET 6 AA410 TYR B 573 LEU B 576 1 O LYS B 575 N VAL B 553 SHEET 7 AA410 THR B 606 ALA B 609 1 O ILE B 608 N LEU B 576 SHEET 8 AA410 VAL B 628 GLN B 630 1 O VAL B 628 N THR B 607 SHEET 9 AA410 PHE B 420 SER B 429 -1 N ASN B 428 O PHE B 629 SHEET 10 AA410 THR B 434 LYS B 445 -1 O ALA B 442 N THR B 421 LINK OE2 GLU A 438 MG MG A 703 1555 1555 2.30 LINK OD1 ASN A 492 MG MG A 703 1555 1555 2.32 LINK OE1 GLU A 524 MG MG A 703 1555 1555 2.16 LINK OD1 ASP A 554 MG MG A 703 1555 1555 2.43 LINK OD2 ASP A 554 MG MG A 703 1555 1555 2.27 LINK O2P C2E A 701 MG MG A 703 1555 1555 2.15 LINK OE2 GLU B 438 MG MG B 703 1555 1555 2.13 LINK OD1 ASN B 492 MG MG B 703 1555 1555 2.09 LINK OE1 GLU B 524 MG MG B 703 1555 1555 2.30 LINK OD2 ASP B 554 MG MG B 703 1555 1555 2.28 LINK O2P C2E B 701 MG MG B 703 1555 1555 2.12 LINK MG MG B 703 O HOH B 804 1555 1555 2.21 SITE 1 AC1 21 ARG A 423 GLN A 425 GLU A 438 PHE A 440 SITE 2 AC1 21 SER A 441 ALA A 452 ASN A 453 LEU A 456 SITE 3 AC1 21 PHE A 468 ASP A 469 ASN A 492 ALA A 494 SITE 4 AC1 21 ASP A 554 ARG A 611 VAL A 612 GLU A 613 SITE 5 AC1 21 GLY A 631 PHE A 632 MG A 703 HOH A 803 SITE 6 AC1 21 HOH A 808 SITE 1 AC2 12 ARG A 248 GLU A 316 THR A 369 LEU A 372 SITE 2 AC2 12 SER A 373 ASP A 376 GLY A 403 LYS A 404 SITE 3 AC2 12 GLN A 405 HOH A 814 TYR B 284 ASP B 288 SITE 1 AC3 5 GLU A 438 ASN A 492 GLU A 524 ASP A 554 SITE 2 AC3 5 C2E A 701 SITE 1 AC4 22 ARG B 423 GLN B 425 GLU B 438 PHE B 440 SITE 2 AC4 22 SER B 441 ALA B 452 ASN B 453 LEU B 456 SITE 3 AC4 22 PHE B 468 ASP B 469 ASN B 492 ALA B 494 SITE 4 AC4 22 ASP B 554 ARG B 611 VAL B 612 GLU B 613 SITE 5 AC4 22 GLY B 631 PHE B 632 MG B 703 HOH B 804 SITE 6 AC4 22 HOH B 808 HOH B 812 SITE 1 AC5 13 TYR A 284 ASP A 288 ARG B 248 ILE B 269 SITE 2 AC5 13 GLU B 316 THR B 369 LEU B 372 SER B 373 SITE 3 AC5 13 ASP B 376 GLY B 403 LYS B 404 GLN B 405 SITE 4 AC5 13 HOH B 809 SITE 1 AC6 6 GLU B 438 ASN B 492 GLU B 524 ASP B 554 SITE 2 AC6 6 C2E B 701 HOH B 804 CRYST1 77.379 90.221 82.750 90.00 115.49 90.00 P 1 21 1 4 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 0.012923 0.000000 0.006161 0.00000 SCALE2 0.000000 0.011084 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013388 0.00000