HEADER TRANSFERASE 20-SEP-11 3TVK TITLE DIGUANYLATE CYCLASE DOMAIN OF DGCZ COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIGUANYLATE CYCLASE DGCZ; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 127-296; COMPND 5 SYNONYM: DGC; COMPND 6 EC: 2.7.7.65; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: B1535, JW1528, YDEG, YDEH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS DIGUANYLATE CYCLASE, PUTATIVE ZINC SENSOR, C-DI-GMP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.ZAEHRINGER,T.SCHIRMER REVDAT 4 13-SEP-23 3TVK 1 REMARK SEQADV HETSYN LINK REVDAT 3 27-APR-16 3TVK 1 COMPND TITLE REVDAT 2 13-APR-16 3TVK 1 JRNL REVDAT 1 03-OCT-12 3TVK 0 JRNL AUTH F.ZAHRINGER,E.LACANNA,U.JENAL,T.SCHIRMER,A.BOEHM JRNL TITL STRUCTURE AND SIGNALING MECHANISM OF A ZINC-SENSORY JRNL TITL 2 DIGUANYLATE CYCLASE. JRNL REF STRUCTURE V. 21 1149 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23769666 JRNL DOI 10.1016/J.STR.2013.04.026 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17232 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 872 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1207 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1370 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 121 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.21000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.32000 REMARK 3 B12 (A**2) : -0.11000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.220 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1550 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 999 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2132 ; 1.281 ; 2.058 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2356 ; 0.804 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 181 ; 5.523 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;34.862 ;23.158 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 241 ;11.863 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;13.563 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 241 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1680 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 313 ; 0.001 ; 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): 866 ; 1.815 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 356 ; 0.681 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1403 ; 2.894 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 684 ; 4.094 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 724 ; 6.019 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3TVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17292 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 51.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34600 REMARK 200 R SYM FOR SHELL (I) : 0.34600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.600 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: PDB ENTRY 1W25 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS, 22.5% PEG 4000, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 34.13800 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 17.06900 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 0.00000 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 34.13800 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 17.06900 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLU A 298 REMARK 465 HIS A 299 REMARK 465 HIS A 300 REMARK 465 HIS A 301 REMARK 465 HIS A 302 REMARK 465 HIS A 303 REMARK 465 HIS A 304 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 155 CD OE1 OE2 REMARK 480 LYS A 170 CD CE NZ REMARK 480 LEU A 179 CG CD1 CD2 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 ARG A 281 -176.70 68.00 REMARK 500 ARG A 281 -176.61 67.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 AUTHORS STATE THAT ONLY HALF OF RESIDUE C2E A 501 HAS BEEN MODELED. REMARK 600 THE OTHER HALF OF THE 2-FOLD SYMMETRIC C2E LIGAND IS GENERATED BY A REMARK 600 CRYSTALLOGRAPHIC 2-FOLD AXIS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 TAR A 505 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 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 198 OD2 REMARK 620 2 C2E A 502 O1P 90.8 REMARK 620 3 HOH A 678 O 170.5 88.7 REMARK 620 4 HOH A 680 O 79.5 94.9 91.1 REMARK 620 5 HOH A 685 O 102.8 84.8 86.6 177.6 REMARK 620 6 HOH A 723 O 86.5 173.3 94.9 90.6 89.9 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAR A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T9O RELATED DB: PDB DBREF 3TVK A 127 296 UNP P31129 YDEH_ECOLI 127 296 SEQADV 3TVK ALA A 126 UNP P31129 EXPRESSION TAG SEQADV 3TVK LEU A 297 UNP P31129 EXPRESSION TAG SEQADV 3TVK GLU A 298 UNP P31129 EXPRESSION TAG SEQADV 3TVK HIS A 299 UNP P31129 EXPRESSION TAG SEQADV 3TVK HIS A 300 UNP P31129 EXPRESSION TAG SEQADV 3TVK HIS A 301 UNP P31129 EXPRESSION TAG SEQADV 3TVK HIS A 302 UNP P31129 EXPRESSION TAG SEQADV 3TVK HIS A 303 UNP P31129 EXPRESSION TAG SEQADV 3TVK HIS A 304 UNP P31129 EXPRESSION TAG SEQRES 1 A 179 ALA ILE ARG SER ASN MET ASP VAL LEU THR GLY LEU PRO SEQRES 2 A 179 GLY ARG ARG VAL LEU ASP GLU SER PHE ASP HIS GLN LEU SEQRES 3 A 179 ARG ASN ALA GLU PRO LEU ASN LEU TYR LEU MET LEU LEU SEQRES 4 A 179 ASP ILE ASP ARG PHE LYS LEU VAL ASN ASP THR TYR GLY SEQRES 5 A 179 HIS LEU ILE GLY ASP VAL VAL LEU ARG THR LEU ALA THR SEQRES 6 A 179 TYR LEU ALA SER TRP THR ARG ASP TYR GLU THR VAL TYR SEQRES 7 A 179 ARG TYR GLY GLY GLU GLU PHE ILE ILE ILE VAL LYS ALA SEQRES 8 A 179 ALA ASN ASP GLU GLU ALA CYS ARG ALA GLY VAL ARG ILE SEQRES 9 A 179 CYS GLN LEU VAL ASP ASN HIS ALA ILE THR HIS SER GLU SEQRES 10 A 179 GLY HIS ILE ASN ILE THR VAL THR ALA GLY VAL SER ARG SEQRES 11 A 179 ALA PHE PRO GLU GLU PRO LEU ASP VAL VAL ILE GLY ARG SEQRES 12 A 179 ALA ASP ARG ALA MET TYR GLU GLY LYS GLN THR GLY ARG SEQRES 13 A 179 ASN ARG CYS MET PHE ILE ASP GLU GLN ASN VAL ILE ASN SEQRES 14 A 179 ARG VAL LEU GLU HIS HIS HIS HIS HIS HIS HET C2E A 501 23 HET C2E A 502 46 HET C2E A 503 46 HET MG A 504 1 HET TAR A 505 5 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 HETNAM TAR D(-)-TARTARIC ACID HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 2 C2E 3(C20 H24 N10 O14 P2) FORMUL 5 MG MG 2+ FORMUL 6 TAR C4 H6 O6 FORMUL 7 HOH *140(H2 O) HELIX 1 1 GLY A 139 ASN A 153 1 15 HELIX 2 2 ARG A 168 GLY A 177 1 10 HELIX 3 3 GLY A 177 TRP A 195 1 19 HELIX 4 4 ASN A 218 HIS A 236 1 19 HELIX 5 5 PRO A 261 THR A 279 1 19 SHEET 1 A 6 VAL A 202 ARG A 204 0 SHEET 2 A 6 GLU A 209 ALA A 216 -1 O ILE A 211 N TYR A 203 SHEET 3 A 6 ASN A 158 ILE A 166 -1 N TYR A 160 O VAL A 214 SHEET 4 A 6 VAL A 249 ALA A 256 -1 O GLY A 252 N LEU A 163 SHEET 5 A 6 ARG A 283 ILE A 287 1 O ARG A 283 N ALA A 251 SHEET 6 A 6 ILE A 293 ARG A 295 -1 O ASN A 294 N PHE A 286 SHEET 1 B 2 ILE A 238 HIS A 240 0 SHEET 2 B 2 GLY A 243 ILE A 245 -1 O ILE A 245 N ILE A 238 LINK P1 C2E A 501 O3' C2E A 501 1555 4665 1.65 LINK OD2 ASP A 198 MG MG A 504 1555 1555 2.22 LINK O1P C2E A 502 MG MG A 504 1555 1555 2.04 LINK MG MG A 504 O HOH A 678 1555 1555 2.24 LINK MG MG A 504 O HOH A 680 1555 1555 2.03 LINK MG MG A 504 O HOH A 685 1555 1555 2.32 LINK MG MG A 504 O HOH A 723 1555 1555 2.03 CISPEP 1 GLU A 155 PRO A 156 0 7.80 SITE 1 AC1 12 PHE A 169 LYS A 170 ASN A 173 HIS A 178 SITE 2 AC1 12 GLY A 181 ASP A 182 LEU A 185 ARG A 204 SITE 3 AC1 12 GLY A 207 GLU A 208 HOH A 641 HOH A 732 SITE 1 AC2 25 SER A 194 TRP A 195 THR A 196 ARG A 197 SITE 2 AC2 25 ASP A 198 ARG A 228 ASP A 270 ARG A 271 SITE 3 AC2 25 TYR A 274 GLU A 275 GLN A 278 ILE A 293 SITE 4 AC2 25 C2E A 503 MG A 504 HOH A 615 HOH A 620 SITE 5 AC2 25 HOH A 636 HOH A 678 HOH A 680 HOH A 685 SITE 6 AC2 25 HOH A 714 HOH A 717 HOH A 726 HOH A 729 SITE 7 AC2 25 HOH A 734 SITE 1 AC3 17 ALA A 126 ARG A 197 GLU A 200 LYS A 215 SITE 2 AC3 17 GLU A 221 ARG A 224 ALA A 225 ARG A 228 SITE 3 AC3 17 ARG A 271 C2E A 502 HOH A 604 HOH A 607 SITE 4 AC3 17 HOH A 609 HOH A 638 HOH A 711 HOH A 727 SITE 5 AC3 17 HOH A 738 SITE 1 AC4 6 ASP A 198 C2E A 502 HOH A 678 HOH A 680 SITE 2 AC4 6 HOH A 685 HOH A 723 SITE 1 AC5 6 ARG A 168 SER A 194 TRP A 195 HIS A 236 SITE 2 AC5 6 GLY A 280 HOH A 739 CRYST1 79.623 79.623 51.207 90.00 90.00 120.00 P 62 6 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 0.012559 0.007251 0.000000 0.00000 SCALE2 0.000000 0.014502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019529 0.00000