HEADER SIGNALING PROTEIN 13-AUG-18 6HBZ TITLE BDELLOVIBRIO BACTERIOVORUS DGCB FULL-LENGTH COMPND MOL_ID: 1; COMPND 2 MOLECULE: GGDEF DOMAIN PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BDELLOVIBRIO BACTERIOVORUS (STRAIN ATCC 15356 / SOURCE 3 DSM 50701 / NCIB 9529 / HD100); SOURCE 4 ORGANISM_TAXID: 264462; SOURCE 5 STRAIN: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100; SOURCE 6 GENE: BD0742; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS GGDEF, FHA, C-DI-GMP, DIGUANYLATE CYCLASE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.L.LOVERING,R.W.MEEK REVDAT 3 15-MAY-24 6HBZ 1 HETSYN REVDAT 2 06-NOV-19 6HBZ 1 JRNL REVDAT 1 28-AUG-19 6HBZ 0 JRNL AUTH R.W.MEEK,I.T.CADBY,P.J.MOYNIHAN,A.L.LOVERING JRNL TITL STRUCTURAL BASIS FOR ACTIVATION OF A DIGUANYLATE CYCLASE JRNL TITL 2 REQUIRED FOR BACTERIAL PREDATION IN BDELLOVIBRIO. JRNL REF NAT COMMUN V. 10 4086 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31501441 JRNL DOI 10.1038/S41467-019-12051-6 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 153.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 92403 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 5021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4156 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 439 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.51000 REMARK 3 B22 (A**2) : -1.51000 REMARK 3 B33 (A**2) : 4.90000 REMARK 3 B12 (A**2) : -0.76000 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): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.706 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6HBZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011452. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-15 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 : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97476 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 153.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 37.00 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 36.90 REMARK 200 R MERGE FOR SHELL (I) : 1.95800 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M KBR, 0.1M SODIUM ACETATE, 15% PEG REMARK 280 4000, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 74.74467 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 37.37233 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 56.05850 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 18.68617 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 93.43083 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 74.74467 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 37.37233 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 18.68617 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 56.05850 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 93.43083 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: 5780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 ILE A 135 REMARK 465 GLU A 136 REMARK 465 ALA A 137 REMARK 465 MET A 138 REMARK 465 THR A 139 REMARK 465 ASN A 140 REMARK 465 ALA A 141 REMARK 465 ALA A 142 REMARK 465 MET A 143 REMARK 465 ALA A 310 REMARK 465 ILE B 135 REMARK 465 GLU B 136 REMARK 465 ALA B 137 REMARK 465 MET B 138 REMARK 465 THR B 139 REMARK 465 ASN B 140 REMARK 465 ALA B 141 REMARK 465 ALA B 142 REMARK 465 MET B 143 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE B 81 O HOH B 501 1.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 609 O HOH B 609 9555 0.53 REMARK 500 O2 EDO B 405 O2 EDO B 405 9555 1.96 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 93 41.69 -106.25 REMARK 500 LYS A 98 159.63 79.44 REMARK 500 ASP A 145 -159.47 -68.76 REMARK 500 ARG A 303 178.19 68.21 REMARK 500 ILE B 52 78.47 -102.00 REMARK 500 ASP B 56 24.24 83.87 REMARK 500 LEU B 93 41.98 -107.36 REMARK 500 LYS B 98 161.19 77.73 REMARK 500 ARG B 303 -178.34 60.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 768 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A 769 DISTANCE = 6.65 ANGSTROMS 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C2E A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 407 DBREF 6HBZ A 32 310 UNP Q6MPU8 Q6MPU8_BDEBA 42 320 DBREF 6HBZ B 32 310 UNP Q6MPU8 Q6MPU8_BDEBA 42 320 SEQRES 1 A 279 VAL PRO PRO ALA ILE VAL VAL LEU ILE GLY PRO PRO GLY SEQRES 2 A 279 TYR VAL GLY LYS GLN TYR PRO ILE THR ALA SER ASP ILE SEQRES 3 A 279 VAL ILE GLY ARG SER VAL GLU SER GLN VAL TYR ILE ASP SEQRES 4 A 279 ASP LYS SER LEU SER ARG SER HIS ALA LYS PHE ALA VAL SEQRES 5 A 279 ASN GLY SER GLU VAL SER VAL ILE ASP LEU GLY SER THR SEQRES 6 A 279 ASN LYS THR ILE VAL ASN GLY GLN VAL ILE PRO PRO LEU SEQRES 7 A 279 ALA SER CYS LEU LEU LYS ASN ASN ASP GLN ILE LYS THR SEQRES 8 A 279 GLY ASN VAL ILE PHE LYS PHE LEU GLU LYS GLY SER ILE SEQRES 9 A 279 GLU ALA MET THR ASN ALA ALA MET TYR ASP ARG ALA GLN SEQRES 10 A 279 LYS ASP ALA LEU THR GLY ALA HIS SER LYS GLY ALA LEU SEQRES 11 A 279 LEU ASP LYS GLY PRO GLU ALA MET LYS ARG ALA GLU VAL SEQRES 12 A 279 LEU ASN GLU PRO PHE SER LEU VAL THR PHE ASP ILE ASP SEQRES 13 A 279 HIS PHE LYS LYS ILE ASN ASP SER TYR GLY HIS PRO GLY SEQRES 14 A 279 GLY ASP TYR VAL LEU LYS GLU LEU CYS ARG ILE VAL ILE SEQRES 15 A 279 THR LYS LEU ILE ARG SER ASN ASP PHE PHE ALA ARG TYR SEQRES 16 A 279 GLY GLY GLU GLU PHE VAL LEU LEU LEU SER GLY SER PRO SEQRES 17 A 279 SER LYS THR ALA GLY GLU VAL GLY GLU ARG ILE ARG GLN SEQRES 18 A 279 THR ILE GLU ALA HIS ASP PHE THR PHE GLU GLY LYS LYS SEQRES 19 A 279 ILE PRO VAL THR ILE SER VAL GLY VAL ALA THR LYS LEU SEQRES 20 A 279 PRO ASN GLU THR GLU TRP THR GLN VAL TYR ASP ARG ALA SEQRES 21 A 279 ASP LYS ALA LEU TYR GLN SER LYS GLN GLY GLY ARG ASN SEQRES 22 A 279 ARG THR THR ILE VAL ALA SEQRES 1 B 279 VAL PRO PRO ALA ILE VAL VAL LEU ILE GLY PRO PRO GLY SEQRES 2 B 279 TYR VAL GLY LYS GLN TYR PRO ILE THR ALA SER ASP ILE SEQRES 3 B 279 VAL ILE GLY ARG SER VAL GLU SER GLN VAL TYR ILE ASP SEQRES 4 B 279 ASP LYS SER LEU SER ARG SER HIS ALA LYS PHE ALA VAL SEQRES 5 B 279 ASN GLY SER GLU VAL SER VAL ILE ASP LEU GLY SER THR SEQRES 6 B 279 ASN LYS THR ILE VAL ASN GLY GLN VAL ILE PRO PRO LEU SEQRES 7 B 279 ALA SER CYS LEU LEU LYS ASN ASN ASP GLN ILE LYS THR SEQRES 8 B 279 GLY ASN VAL ILE PHE LYS PHE LEU GLU LYS GLY SER ILE SEQRES 9 B 279 GLU ALA MET THR ASN ALA ALA MET TYR ASP ARG ALA GLN SEQRES 10 B 279 LYS ASP ALA LEU THR GLY ALA HIS SER LYS GLY ALA LEU SEQRES 11 B 279 LEU ASP LYS GLY PRO GLU ALA MET LYS ARG ALA GLU VAL SEQRES 12 B 279 LEU ASN GLU PRO PHE SER LEU VAL THR PHE ASP ILE ASP SEQRES 13 B 279 HIS PHE LYS LYS ILE ASN ASP SER TYR GLY HIS PRO GLY SEQRES 14 B 279 GLY ASP TYR VAL LEU LYS GLU LEU CYS ARG ILE VAL ILE SEQRES 15 B 279 THR LYS LEU ILE ARG SER ASN ASP PHE PHE ALA ARG TYR SEQRES 16 B 279 GLY GLY GLU GLU PHE VAL LEU LEU LEU SER GLY SER PRO SEQRES 17 B 279 SER LYS THR ALA GLY GLU VAL GLY GLU ARG ILE ARG GLN SEQRES 18 B 279 THR ILE GLU ALA HIS ASP PHE THR PHE GLU GLY LYS LYS SEQRES 19 B 279 ILE PRO VAL THR ILE SER VAL GLY VAL ALA THR LYS LEU SEQRES 20 B 279 PRO ASN GLU THR GLU TRP THR GLN VAL TYR ASP ARG ALA SEQRES 21 B 279 ASP LYS ALA LEU TYR GLN SER LYS GLN GLY GLY ARG ASN SEQRES 22 B 279 ARG THR THR ILE VAL ALA HET C2E A 401 46 HET C2E A 402 46 HET CL A 403 1 HET CL A 404 1 HET CL B 401 1 HET CL B 402 1 HET CL B 403 1 HET EDO B 404 4 HET EDO B 405 4 HET EDO B 406 4 HET EDO B 407 4 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 CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 C2E 2(C20 H24 N10 O14 P2) FORMUL 5 CL 5(CL 1-) FORMUL 10 EDO 4(C2 H6 O2) FORMUL 14 HOH *439(H2 O) HELIX 1 AA1 ASP A 145 GLY A 154 1 10 HELIX 2 AA2 ALA A 160 ASN A 176 1 17 HELIX 3 AA3 HIS A 188 GLY A 197 1 10 HELIX 4 AA4 GLY A 197 LEU A 216 1 20 HELIX 5 AA5 PRO A 239 HIS A 257 1 19 HELIX 6 AA6 GLU A 283 GLY A 301 1 19 HELIX 7 AA7 SER B 157 ASN B 176 1 20 HELIX 8 AA8 HIS B 188 GLY B 197 1 10 HELIX 9 AA9 GLY B 197 LEU B 216 1 20 HELIX 10 AB1 PRO B 239 HIS B 257 1 19 HELIX 11 AB2 GLU B 283 GLY B 301 1 19 SHEET 1 AA1 6 GLN A 49 PRO A 51 0 SHEET 2 AA1 6 ALA A 35 ILE A 40 -1 N ILE A 36 O TYR A 50 SHEET 3 AA1 6 VAL A 125 LEU A 130 -1 O LEU A 130 N ALA A 35 SHEET 4 AA1 6 GLN A 119 THR A 122 -1 N ILE A 120 O PHE A 127 SHEET 5 AA1 6 THR A 99 VAL A 101 -1 N ILE A 100 O LYS A 121 SHEET 6 AA1 6 GLN A 104 ILE A 106 -1 O ILE A 106 N THR A 99 SHEET 1 AA2 5 VAL A 67 TYR A 68 0 SHEET 2 AA2 5 VAL A 58 GLY A 60 1 N VAL A 58 O VAL A 67 SHEET 3 AA2 5 ALA A 79 ASN A 84 -1 O ALA A 79 N ILE A 59 SHEET 4 AA2 5 GLU A 87 ASP A 92 -1 O GLU A 87 N ASN A 84 SHEET 5 AA2 5 SER A 111 LEU A 113 -1 O CYS A 112 N VAL A 90 SHEET 1 AA3 5 PHE A 222 TYR A 226 0 SHEET 2 AA3 5 GLU A 230 SER A 236 -1 O LEU A 234 N PHE A 222 SHEET 3 AA3 5 PHE A 179 ILE A 186 -1 N SER A 180 O LEU A 235 SHEET 4 AA3 5 ILE A 270 THR A 276 -1 O GLY A 273 N THR A 183 SHEET 5 AA3 5 THR A 306 ILE A 308 1 O THR A 307 N VAL A 274 SHEET 1 AA4 2 PHE A 259 PHE A 261 0 SHEET 2 AA4 2 LYS A 264 ILE A 266 -1 O ILE A 266 N PHE A 259 SHEET 1 AA5 6 GLN B 49 PRO B 51 0 SHEET 2 AA5 6 ALA B 35 ILE B 40 -1 N ILE B 36 O TYR B 50 SHEET 3 AA5 6 VAL B 125 LEU B 130 -1 O LEU B 130 N ALA B 35 SHEET 4 AA5 6 GLN B 119 THR B 122 -1 N ILE B 120 O PHE B 127 SHEET 5 AA5 6 THR B 99 VAL B 101 -1 N ILE B 100 O LYS B 121 SHEET 6 AA5 6 GLN B 104 ILE B 106 -1 O ILE B 106 N THR B 99 SHEET 1 AA6 5 VAL B 67 TYR B 68 0 SHEET 2 AA6 5 VAL B 58 GLY B 60 1 N VAL B 58 O VAL B 67 SHEET 3 AA6 5 ALA B 79 ASN B 84 -1 O ALA B 79 N ILE B 59 SHEET 4 AA6 5 GLU B 87 ASP B 92 -1 O GLU B 87 N ASN B 84 SHEET 5 AA6 5 SER B 111 LEU B 113 -1 O CYS B 112 N VAL B 90 SHEET 1 AA7 5 PHE B 222 ARG B 225 0 SHEET 2 AA7 5 GLU B 230 SER B 236 -1 O LEU B 234 N PHE B 222 SHEET 3 AA7 5 PHE B 179 ILE B 186 -1 N SER B 180 O LEU B 235 SHEET 4 AA7 5 ILE B 270 THR B 276 -1 O GLY B 273 N THR B 183 SHEET 5 AA7 5 THR B 306 ILE B 308 1 O THR B 307 N VAL B 274 SHEET 1 AA8 2 PHE B 259 PHE B 261 0 SHEET 2 AA8 2 LYS B 264 ILE B 266 -1 O ILE B 266 N PHE B 259 SITE 1 AC1 20 LYS A 215 LEU A 216 ILE A 217 ARG A 218 SITE 2 AC1 20 SER A 219 ARG A 249 C2E A 402 HOH A 517 SITE 3 AC1 20 HOH A 539 HOH A 561 HOH A 598 HOH A 602 SITE 4 AC1 20 HOH A 609 HOH A 642 ARG B 218 ASP B 221 SITE 5 AC1 20 THR B 242 ARG B 249 HOH B 504 HOH B 507 SITE 1 AC2 21 ILE A 217 ARG A 218 ASP A 221 THR A 242 SITE 2 AC2 21 VAL A 246 ARG A 249 C2E A 401 HOH A 502 SITE 3 AC2 21 HOH A 547 HOH A 577 HOH A 578 HOH A 604 SITE 4 AC2 21 HOH A 609 HOH A 652 HOH A 667 LYS B 215 SITE 5 AC2 21 LEU B 216 ILE B 217 ARG B 218 SER B 219 SITE 6 AC2 21 ARG B 249 SITE 1 AC3 3 PRO A 166 GLU A 283 TRP A 284 SITE 1 AC4 3 ARG A 76 ASP B 56 CL B 403 SITE 1 AC5 3 ARG B 61 ARG B 76 HOH B 633 SITE 1 AC6 2 HIS B 188 ARG B 303 SITE 1 AC7 4 ARG A 76 SER A 77 CL A 404 LYS B 80 SITE 1 AC8 6 SER B 240 THR B 276 LEU B 278 HOH B 517 SITE 2 AC8 6 HOH B 540 HOH B 588 SITE 1 AC9 3 ASP B 202 ARG B 225 HOH B 509 SITE 1 AD1 3 ILE B 100 LYS B 121 HOH B 599 SITE 1 AD2 2 GLY B 154 THR B 214 CRYST1 176.776 176.776 112.117 90.00 90.00 120.00 P 65 2 2 24 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 0.005657 0.003266 0.000000 0.00000 SCALE2 0.000000 0.006532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008919 0.00000