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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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