HEADER TRANSFERASE 18-SEP-12 4H54 TITLE CRYSTAL STRUCTURE OF THE DIGUANYLATE CYCLASE DGCZ COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIGUANYLATE CYCLASE YDEH; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DGCZ, DGC; COMPND 5 EC: 2.7.7.65; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B1535, JW1528, YDEG, YDEH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS ZINC SENSOR, C-DI-GMP, CZB DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.ZAEHRINGER,T.SCHIRMER REVDAT 3 20-SEP-23 4H54 1 REMARK SEQADV HETSYN LINK REVDAT 2 17-JUL-13 4H54 1 JRNL REVDAT 1 03-JUL-13 4H54 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. 3.90 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) : 3.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 7072 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) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 335 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 4.36 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.76 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1994 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2391 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1892 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE : 0.2411 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.12 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 102 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4348 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 162 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 104.9 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -21.37470 REMARK 3 B22 (A**2) : -21.37470 REMARK 3 B33 (A**2) : 42.74950 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.846 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.716 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.706 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.660 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4613 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 6297 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1613 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 120 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 656 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4613 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 4 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 605 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5723 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 1.04 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.69 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.60 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|5 - A|35 A|54 - A|126 A|400 } REMARK 3 ORIGIN FOR THE GROUP (A): 75.1225 -28.0243 -0.0934 REMARK 3 T TENSOR REMARK 3 T11: -0.2413 T22: -0.1783 REMARK 3 T33: -0.1768 T12: 0.5825 REMARK 3 T13: 0.1972 T23: -0.0543 REMARK 3 L TENSOR REMARK 3 L11: 22.0220 L22: 1.8834 REMARK 3 L33: 6.5377 L12: 2.6762 REMARK 3 L13: -0.2496 L23: 5.6069 REMARK 3 S TENSOR REMARK 3 S11: 0.5997 S12: -1.2916 S13: -1.6904 REMARK 3 S21: 1.6391 S22: -1.1793 S23: -1.0037 REMARK 3 S31: -0.1124 S32: 0.6492 S33: 0.5797 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|127 - A|296 A|600 A|601 A|700 A|701 } REMARK 3 ORIGIN FOR THE GROUP (A): 32.3592 -41.5974 6.2266 REMARK 3 T TENSOR REMARK 3 T11: -1.0546 T22: -0.4067 REMARK 3 T33: -1.0341 T12: -0.8601 REMARK 3 T13: -0.3722 T23: 0.0293 REMARK 3 L TENSOR REMARK 3 L11: 9.5482 L22: 16.3911 REMARK 3 L33: 11.9367 L12: -0.3882 REMARK 3 L13: -0.2998 L23: 0.1041 REMARK 3 S TENSOR REMARK 3 S11: 0.2104 S12: 0.2438 S13: -0.6238 REMARK 3 S21: -1.0938 S22: -0.1676 S23: 0.6109 REMARK 3 S31: 1.8571 S32: 0.4205 S33: -0.0428 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { B|2 - B|35 B|65 - B|126 B|400 } REMARK 3 ORIGIN FOR THE GROUP (A): 69.1571 -11.1277 -3.9320 REMARK 3 T TENSOR REMARK 3 T11: -0.4696 T22: -1.1023 REMARK 3 T33: 0.2237 T12: 0.7201 REMARK 3 T13: 0.2998 T23: -0.0760 REMARK 3 L TENSOR REMARK 3 L11: 30.4169 L22: -5.1543 REMARK 3 L33: 1.6239 L12: 4.3169 REMARK 3 L13: -0.1060 L23: 6.9736 REMARK 3 S TENSOR REMARK 3 S11: 0.7992 S12: -1.1560 S13: 2.9013 REMARK 3 S21: 2.1379 S22: -1.9526 S23: -1.1317 REMARK 3 S31: -1.3915 S32: 2.3174 S33: 1.1535 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { B|127 - B|296 B|600 B|601 B|700} REMARK 3 ORIGIN FOR THE GROUP (A): 29.9366 -18.6675 -9.5784 REMARK 3 T TENSOR REMARK 3 T11: -0.2507 T22: -0.4045 REMARK 3 T33: -1.4479 T12: -0.4411 REMARK 3 T13: -0.2855 T23: -0.2478 REMARK 3 L TENSOR REMARK 3 L11: 7.0653 L22: 15.7840 REMARK 3 L33: 9.9917 L12: 1.7620 REMARK 3 L13: -1.5672 L23: -0.7662 REMARK 3 S TENSOR REMARK 3 S11: 0.2270 S12: -0.2160 S13: 0.8827 REMARK 3 S21: -1.5795 S22: 0.3185 S23: 0.5167 REMARK 3 S31: 0.3619 S32: -1.1263 S33: -0.5455 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4H54 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000075030. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 1.0000 REMARK 200 MONOCHROMATOR : BARTELS 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7076 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.900 REMARK 200 RESOLUTION RANGE LOW (A) : 89.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.93 REMARK 200 R MERGE FOR SHELL (I) : 0.77000 REMARK 200 R SYM FOR SHELL (I) : 0.83000 REMARK 200 FOR SHELL : 1.000 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 ENTRIES 3T90 AND 3TVK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM CALCIUM ACETATE, 20.0% PEG4000, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 43.05200 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 86.10400 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 64.57800 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 107.63000 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 21.52600 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: 7750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 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 ALA A 1 REMARK 465 ILE A 2 REMARK 465 LYS A 3 REMARK 465 LYS A 4 REMARK 465 ARG A 36 REMARK 465 ASP A 37 REMARK 465 ALA A 38 REMARK 465 SER A 39 REMARK 465 LYS A 40 REMARK 465 PRO A 41 REMARK 465 GLU A 42 REMARK 465 ILE A 43 REMARK 465 THR A 44 REMARK 465 ASP A 45 REMARK 465 ASN A 46 REMARK 465 HIS A 47 REMARK 465 SER A 48 REMARK 465 TYR A 49 REMARK 465 GLY A 50 REMARK 465 LEU A 51 REMARK 465 ALA A 52 REMARK 465 GLN A 53 REMARK 465 LEU A 297 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 465 ASP B 37 REMARK 465 ALA B 38 REMARK 465 SER B 39 REMARK 465 LYS B 40 REMARK 465 PRO B 41 REMARK 465 GLU B 42 REMARK 465 ILE B 43 REMARK 465 THR B 44 REMARK 465 ASP B 45 REMARK 465 ASN B 46 REMARK 465 HIS B 47 REMARK 465 SER B 48 REMARK 465 TYR B 49 REMARK 465 GLY B 50 REMARK 465 LEU B 51 REMARK 465 ALA B 52 REMARK 465 GLN B 53 REMARK 465 PHE B 54 REMARK 465 GLY B 55 REMARK 465 ARG B 56 REMARK 465 TRP B 57 REMARK 465 ILE B 58 REMARK 465 ASP B 59 REMARK 465 HIS B 60 REMARK 465 LEU B 61 REMARK 465 GLY B 62 REMARK 465 PRO B 63 REMARK 465 LEU B 64 REMARK 465 GLU B 298 REMARK 465 HIS B 299 REMARK 465 HIS B 300 REMARK 465 HIS B 301 REMARK 465 HIS B 302 REMARK 465 HIS B 303 REMARK 465 HIS B 304 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 GLU A 7 CG CD OE1 OE2 REMARK 470 ARG A 56 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 108 CG CD OE1 OE2 REMARK 470 GLU B 108 CG CD OE1 OE2 REMARK 470 LEU B 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 HIS A 60 38.12 -97.41 REMARK 500 PRO A 63 113.07 -22.22 REMARK 500 LEU A 64 -144.85 -86.14 REMARK 500 HIS A 97 46.81 -153.32 REMARK 500 ARG A 281 176.26 84.59 REMARK 500 LYS B 3 174.79 47.24 REMARK 500 LYS B 4 113.39 52.34 REMARK 500 HIS B 97 46.11 -152.88 REMARK 500 ASN B 130 20.63 -78.30 REMARK 500 ARG B 281 176.25 84.36 REMARK 500 REMARK 500 REMARK: NULL 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 GAV A 404 REMARK 610 GAV B 404 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 22 NE2 REMARK 620 2 HIS A 79 NE2 79.3 REMARK 620 3 HIS A 83 NE2 88.6 81.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 165 OD2 REMARK 620 2 ILE A 166 O 94.4 REMARK 620 3 GLU A 208 OE2 72.3 120.7 REMARK 620 4 GLU A 208 OE1 91.6 71.7 52.1 REMARK 620 5 GAV A 402 O3G 121.1 97.4 139.5 146.7 REMARK 620 6 GAV A 402 O2B 161.8 72.1 103.7 72.9 73.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 22 NE2 REMARK 620 2 HIS B 79 NE2 86.6 REMARK 620 3 HIS B 83 NE2 94.3 87.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 165 OD2 REMARK 620 2 ILE B 166 O 88.1 REMARK 620 3 GLU B 208 OE1 80.8 74.4 REMARK 620 4 GLU B 208 OE2 58.5 113.6 47.1 REMARK 620 5 GAV B 402 O2B 151.9 86.8 71.2 98.8 REMARK 620 6 GAV B 402 O3B 119.9 149.6 97.2 76.5 63.0 REMARK 620 7 GAV B 402 O3G 110.1 118.1 162.7 126.6 96.6 66.0 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 ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAV A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAV A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAV B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAV B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T9O RELATED DB: PDB REMARK 900 CZB DOMAIN OF DGCZ REMARK 900 RELATED ID: 3TVK RELATED DB: PDB REMARK 900 GGDEF DOMAIN OF DGCZ DBREF 4H54 A 2 296 UNP P31129 YDEH_ECOLI 2 296 DBREF 4H54 B 2 296 UNP P31129 YDEH_ECOLI 2 296 SEQADV 4H54 ALA A 1 UNP P31129 EXPRESSION TAG SEQADV 4H54 ALA A 52 UNP P31129 CYS 52 ENGINEERED MUTATION SEQADV 4H54 LEU A 297 UNP P31129 EXPRESSION TAG SEQADV 4H54 GLU A 298 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS A 299 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS A 300 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS A 301 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS A 302 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS A 303 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS A 304 UNP P31129 EXPRESSION TAG SEQADV 4H54 ALA B 1 UNP P31129 EXPRESSION TAG SEQADV 4H54 ALA B 52 UNP P31129 CYS 52 ENGINEERED MUTATION SEQADV 4H54 LEU B 297 UNP P31129 EXPRESSION TAG SEQADV 4H54 GLU B 298 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS B 299 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS B 300 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS B 301 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS B 302 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS B 303 UNP P31129 EXPRESSION TAG SEQADV 4H54 HIS B 304 UNP P31129 EXPRESSION TAG SEQRES 1 A 304 ALA ILE LYS LYS THR THR GLU ILE ASP ALA ILE LEU LEU SEQRES 2 A 304 ASN LEU ASN LYS ALA ILE ASP ALA HIS TYR GLN TRP LEU SEQRES 3 A 304 VAL SER MET PHE HIS SER VAL VAL ALA ARG ASP ALA SER SEQRES 4 A 304 LYS PRO GLU ILE THR ASP ASN HIS SER TYR GLY LEU ALA SEQRES 5 A 304 GLN PHE GLY ARG TRP ILE ASP HIS LEU GLY PRO LEU ASP SEQRES 6 A 304 ASN ASP GLU LEU PRO TYR VAL ARG LEU MET ASP SER ALA SEQRES 7 A 304 HIS GLN HIS MET HIS ASN CYS GLY ARG GLU LEU MET LEU SEQRES 8 A 304 ALA ILE VAL GLU ASN HIS TRP GLN ASP ALA HIS PHE ASP SEQRES 9 A 304 ALA PHE GLN GLU GLY LEU LEU SER PHE THR ALA ALA LEU SEQRES 10 A 304 THR ASP TYR LYS ILE TYR LEU LEU THR ILE ARG SER ASN SEQRES 11 A 304 MET ASP VAL LEU THR GLY LEU PRO GLY ARG ARG VAL LEU SEQRES 12 A 304 ASP GLU SER PHE ASP HIS GLN LEU ARG ASN ALA GLU PRO SEQRES 13 A 304 LEU ASN LEU TYR LEU MET LEU LEU ASP ILE ASP ARG PHE SEQRES 14 A 304 LYS LEU VAL ASN ASP THR TYR GLY HIS LEU ILE GLY ASP SEQRES 15 A 304 VAL VAL LEU ARG THR LEU ALA THR TYR LEU ALA SER TRP SEQRES 16 A 304 THR ARG ASP TYR GLU THR VAL TYR ARG TYR GLY GLY GLU SEQRES 17 A 304 GLU PHE ILE ILE ILE VAL LYS ALA ALA ASN ASP GLU GLU SEQRES 18 A 304 ALA CYS ARG ALA GLY VAL ARG ILE CYS GLN LEU VAL ASP SEQRES 19 A 304 ASN HIS ALA ILE THR HIS SER GLU GLY HIS ILE ASN ILE SEQRES 20 A 304 THR VAL THR ALA GLY VAL SER ARG ALA PHE PRO GLU GLU SEQRES 21 A 304 PRO LEU ASP VAL VAL ILE GLY ARG ALA ASP ARG ALA MET SEQRES 22 A 304 TYR GLU GLY LYS GLN THR GLY ARG ASN ARG CYS MET PHE SEQRES 23 A 304 ILE ASP GLU GLN ASN VAL ILE ASN ARG VAL LEU GLU HIS SEQRES 24 A 304 HIS HIS HIS HIS HIS SEQRES 1 B 304 ALA ILE LYS LYS THR THR GLU ILE ASP ALA ILE LEU LEU SEQRES 2 B 304 ASN LEU ASN LYS ALA ILE ASP ALA HIS TYR GLN TRP LEU SEQRES 3 B 304 VAL SER MET PHE HIS SER VAL VAL ALA ARG ASP ALA SER SEQRES 4 B 304 LYS PRO GLU ILE THR ASP ASN HIS SER TYR GLY LEU ALA SEQRES 5 B 304 GLN PHE GLY ARG TRP ILE ASP HIS LEU GLY PRO LEU ASP SEQRES 6 B 304 ASN ASP GLU LEU PRO TYR VAL ARG LEU MET ASP SER ALA SEQRES 7 B 304 HIS GLN HIS MET HIS ASN CYS GLY ARG GLU LEU MET LEU SEQRES 8 B 304 ALA ILE VAL GLU ASN HIS TRP GLN ASP ALA HIS PHE ASP SEQRES 9 B 304 ALA PHE GLN GLU GLY LEU LEU SER PHE THR ALA ALA LEU SEQRES 10 B 304 THR ASP TYR LYS ILE TYR LEU LEU THR ILE ARG SER ASN SEQRES 11 B 304 MET ASP VAL LEU THR GLY LEU PRO GLY ARG ARG VAL LEU SEQRES 12 B 304 ASP GLU SER PHE ASP HIS GLN LEU ARG ASN ALA GLU PRO SEQRES 13 B 304 LEU ASN LEU TYR LEU MET LEU LEU ASP ILE ASP ARG PHE SEQRES 14 B 304 LYS LEU VAL ASN ASP THR TYR GLY HIS LEU ILE GLY ASP SEQRES 15 B 304 VAL VAL LEU ARG THR LEU ALA THR TYR LEU ALA SER TRP SEQRES 16 B 304 THR ARG ASP TYR GLU THR VAL TYR ARG TYR GLY GLY GLU SEQRES 17 B 304 GLU PHE ILE ILE ILE VAL LYS ALA ALA ASN ASP GLU GLU SEQRES 18 B 304 ALA CYS ARG ALA GLY VAL ARG ILE CYS GLN LEU VAL ASP SEQRES 19 B 304 ASN HIS ALA ILE THR HIS SER GLU GLY HIS ILE ASN ILE SEQRES 20 B 304 THR VAL THR ALA GLY VAL SER ARG ALA PHE PRO GLU GLU SEQRES 21 B 304 PRO LEU ASP VAL VAL ILE GLY ARG ALA ASP ARG ALA MET SEQRES 22 B 304 TYR GLU GLY LYS GLN THR GLY ARG ASN ARG CYS MET PHE SEQRES 23 B 304 ILE ASP GLU GLN ASN VAL ILE ASN ARG VAL LEU GLU HIS SEQRES 24 B 304 HIS HIS HIS HIS HIS HET ZN A 401 1 HET GAV A 402 32 HET MG A 403 1 HET GAV A 404 24 HET C2E A 405 46 HET ZN B 401 1 HET GAV B 402 32 HET MG B 403 1 HET GAV B 404 24 HETNAM ZN ZINC ION HETNAM GAV GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION 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) HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 GAV 4(C10 H16 N5 O13 P3 S) FORMUL 5 MG 2(MG 2+) FORMUL 7 C2E C20 H24 N10 O14 P2 HELIX 1 1 THR A 5 ALA A 35 1 31 HELIX 2 2 ILE A 58 GLY A 62 5 5 HELIX 3 3 GLU A 68 GLU A 95 1 28 HELIX 4 4 GLN A 99 ASN A 130 1 32 HELIX 5 5 GLY A 139 ASN A 153 1 15 HELIX 6 6 ARG A 168 GLY A 177 1 10 HELIX 7 7 GLY A 177 THR A 196 1 20 HELIX 8 8 ASN A 218 HIS A 236 1 19 HELIX 9 9 PRO A 261 GLY A 280 1 20 HELIX 10 10 THR B 5 ARG B 36 1 32 HELIX 11 11 GLU B 68 GLU B 95 1 28 HELIX 12 12 GLN B 99 ASN B 130 1 32 HELIX 13 13 GLY B 139 ASN B 153 1 15 HELIX 14 14 ARG B 168 GLY B 177 1 10 HELIX 15 15 GLY B 177 THR B 196 1 20 HELIX 16 16 ASN B 218 HIS B 236 1 19 HELIX 17 17 PRO B 261 GLY B 280 1 20 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 CYS A 284 ILE A 287 1 O MET A 285 N VAL A 253 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 GLY A 243 N HIS A 240 SHEET 1 C 6 VAL B 202 ARG B 204 0 SHEET 2 C 6 GLU B 209 ALA B 216 -1 O ILE B 211 N TYR B 203 SHEET 3 C 6 ASN B 158 ILE B 166 -1 N TYR B 160 O VAL B 214 SHEET 4 C 6 VAL B 249 ALA B 256 -1 O GLY B 252 N LEU B 163 SHEET 5 C 6 CYS B 284 ILE B 287 1 O MET B 285 N VAL B 253 SHEET 6 C 6 ILE B 293 ARG B 295 -1 O ASN B 294 N PHE B 286 SHEET 1 D 2 ILE B 238 HIS B 240 0 SHEET 2 D 2 GLY B 243 ILE B 245 -1 O GLY B 243 N HIS B 240 LINK NE2 HIS A 22 ZN ZN A 401 1555 1555 2.21 LINK NE2 HIS A 79 ZN ZN A 401 1555 1555 2.31 LINK NE2 HIS A 83 ZN ZN A 401 1555 1555 2.12 LINK OD2 ASP A 165 MG MG A 403 1555 1555 1.73 LINK O ILE A 166 MG MG A 403 1555 1555 1.98 LINK OE2 GLU A 208 MG MG A 403 1555 1555 2.45 LINK OE1 GLU A 208 MG MG A 403 1555 1555 2.53 LINK O3G GAV A 402 MG MG A 403 1555 1555 1.86 LINK O2B GAV A 402 MG MG A 403 1555 1555 2.56 LINK NE2 HIS B 22 ZN ZN B 401 1555 1555 2.23 LINK NE2 HIS B 79 ZN ZN B 401 1555 1555 2.10 LINK NE2 HIS B 83 ZN ZN B 401 1555 1555 2.02 LINK OD2 ASP B 165 MG MG B 403 1555 1555 2.20 LINK O ILE B 166 MG MG B 403 1555 1555 1.68 LINK OE1 GLU B 208 MG MG B 403 1555 1555 2.59 LINK OE2 GLU B 208 MG MG B 403 1555 1555 2.87 LINK O2B GAV B 402 MG MG B 403 1555 1555 2.14 LINK O3B GAV B 402 MG MG B 403 1555 1555 2.71 LINK O3G GAV B 402 MG MG B 403 1555 1555 1.67 CISPEP 1 GLU A 155 PRO A 156 0 -0.35 CISPEP 2 ALA B 1 ILE B 2 0 -2.83 CISPEP 3 GLU B 155 PRO B 156 0 0.06 SITE 1 AC1 3 HIS A 22 HIS A 79 HIS A 83 SITE 1 AC2 19 LEU A 134 ASP A 165 ILE A 166 ASP A 167 SITE 2 AC2 19 ARG A 168 PHE A 169 LYS A 170 ASN A 173 SITE 3 AC2 19 HIS A 178 ASP A 182 LEU A 185 ARG A 204 SITE 4 AC2 19 GLY A 207 GLU A 208 LYS A 277 ARG A 281 SITE 5 AC2 19 MG A 403 ARG B 140 TYR B 205 SITE 1 AC3 5 ASP A 165 ILE A 166 GLU A 208 LYS A 277 SITE 2 AC3 5 GAV A 402 SITE 1 AC4 5 GLU A 200 LYS A 215 ALA A 225 ARG A 228 SITE 2 AC4 5 C2E A 405 SITE 1 AC5 14 SER A 194 TRP A 195 THR A 196 ARG A 197 SITE 2 AC5 14 ASP A 198 ARG A 228 GAV A 404 SER B 194 SITE 3 AC5 14 TRP B 195 THR B 196 ARG B 197 ASP B 198 SITE 4 AC5 14 ARG B 228 GAV B 404 SITE 1 AC6 3 HIS B 22 HIS B 79 HIS B 83 SITE 1 AC7 19 ARG A 140 GLU A 209 LEU B 134 ASP B 165 SITE 2 AC7 19 ILE B 166 ASP B 167 ARG B 168 PHE B 169 SITE 3 AC7 19 LYS B 170 ASN B 173 HIS B 178 ASP B 182 SITE 4 AC7 19 LEU B 185 ARG B 204 GLY B 207 GLU B 208 SITE 5 AC7 19 LYS B 277 ARG B 281 MG B 403 SITE 1 AC8 6 ASP B 165 ILE B 166 ASP B 167 GLU B 208 SITE 2 AC8 6 LYS B 277 GAV B 402 SITE 1 AC9 8 C2E A 405 ARG B 197 TYR B 199 GLU B 200 SITE 2 AC9 8 LYS B 215 ARG B 224 ALA B 225 ARG B 228 CRYST1 102.593 102.593 129.156 90.00 90.00 120.00 P 61 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 0.009747 0.005628 0.000000 0.00000 SCALE2 0.000000 0.011255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007743 0.00000