HEADER HYDROLASE 15-DEC-04 1VQ2
TITLE CRYSTAL STRUCTURE OF T4-BACTERIOPHAGE DEOXYCYTIDYLATE DEAMINASE,
TITLE 2 MUTANT R115E
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DEOXYCYTIDYLATE DEAMINASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: DCMP DEAMINASE;
COMPND 5 EC: 3.5.4.12;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4;
SOURCE 3 ORGANISM_TAXID: 10665;
SOURCE 4 GENE: CD;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR R.ALMOG,F.MALEY,G.F.MALEY,R.MACCOLL,P.VAN ROEY
REVDAT 5 27-DEC-23 1VQ2 1 REMARK
REVDAT 4 20-OCT-21 1VQ2 1 REMARK SEQADV LINK
REVDAT 3 13-JUL-11 1VQ2 1 VERSN
REVDAT 2 24-FEB-09 1VQ2 1 VERSN
REVDAT 1 21-DEC-04 1VQ2 0
SPRSDE 21-DEC-04 1VQ2 1TEO
JRNL AUTH R.ALMOG,F.MALEY,G.F.MALEY,R.MACCOLL,P.VAN ROEY
JRNL TITL THREE-DIMENSIONAL STRUCTURE OF THE R115E MUTANT OF
JRNL TITL 2 T4-BACTERIOPHAGE 2'-DEOXYCYTIDYLATE DEAMINASE
JRNL REF BIOCHEMISTRY V. 43 13715 2004
JRNL REFN ISSN 0006-2960
JRNL PMID 15504034
JRNL DOI 10.1021/BI048928H
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 0.9
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.59
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2149024.360
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 15537
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 SET) : 0.218
REMARK 3 FREE R VALUE : 0.245
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800
REMARK 3 FREE R VALUE TEST SET COUNT : 1516
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2266
REMARK 3 BIN R VALUE (WORKING SET) : 0.2760
REMARK 3 BIN FREE R VALUE : 0.3200
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 261
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1320
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 22
REMARK 3 SOLVENT ATOMS : 47
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 23.20
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.60
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.70000
REMARK 3 B22 (A**2) : -0.70000
REMARK 3 B33 (A**2) : 1.39000
REMARK 3 B12 (A**2) : 3.68000
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) : 0.28
REMARK 3 ESD FROM SIGMAA (A) : 0.22
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.006
REMARK 3 BOND ANGLES (DEGREES) : 1.200
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.690
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 0.770 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.330 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.200 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.880 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.40
REMARK 3 BSOL : 35.97
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : PDP_DHZ_OH.PARAM
REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 4 : ION.PARAM
REMARK 3 PARAMETER FILE 5 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : PDP_DHZ_OH.TOP
REMARK 3 TOPOLOGY FILE 4 : ION.TOP
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1VQ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-04.
REMARK 100 THE DEPOSITION ID IS D_1000002050.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-MAY-02
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X12C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.286, 1.2809, 1.000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15589
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0
REMARK 200 DATA REDUNDANCY : 9.700
REMARK 200 R MERGE (I) : 0.04400
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) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 64.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, DTT, SODIUM CITRATE,
REMARK 280 PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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
REMARK 290 3555 -X+Y,-X,Z
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/2
REMARK 290 6555 X-Y,X,Z+1/2
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z
REMARK 290 10555 -Y,-X,-Z+1/2
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+1/2
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 0.00000
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 0.00000
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 38.47500
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 38.47500
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 38.47500
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 0.00000
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 0.00000
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 38.47500
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 38.47500
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 38.47500
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: 3870 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15530 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -113.0 KCAL/MOL
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 350 BIOMT1 2 -1.000000 0.000000 0.000000 114.52800
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 38.47500
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 19760 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 38450 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -375.0 KCAL/MOL
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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 114.52800
REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 57.26400
REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 99.18416
REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 57.26400
REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 99.18416
REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 38.47500
REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 114.52800
REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 38.47500
REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 0.00000
REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 0.00000
REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 38.47500
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 PRO A 63
REMARK 465 LYS A 64
REMARK 465 HIS A 65
REMARK 465 ALA A 66
REMARK 465 ILE A 67
REMARK 465 ILE A 68
REMARK 465 GLN A 69
REMARK 465 GLY A 70
REMARK 465 HIS A 71
REMARK 465 LYS A 72
REMARK 465 PRO A 73
REMARK 465 GLU A 74
REMARK 465 CYS A 75
REMARK 465 VAL A 76
REMARK 465 SER A 77
REMARK 465 PHE A 78
REMARK 465 GLY A 79
REMARK 465 SER A 80
REMARK 465 THR A 81
REMARK 465 ASP A 82
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 LYS A 62 CG CD CE NZ
REMARK 470 ARG A 83 CG CD NE CZ NH1 NH2
REMARK 470 SER A 99 OG
REMARK 470 LYS A 157 CG CD CE NZ
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 A 430 O HOH A 430 11655 2.01
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 GLU A 189 -75.83 -115.70
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 702 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 19 SG
REMARK 620 2 CYS A 49 SG 122.5
REMARK 620 3 HIS A 94 NE2 102.7 101.0
REMARK 620 4 GLU A 102 OE2 118.1 105.4 104.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 701 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 104 ND1
REMARK 620 2 CYS A 132 SG 104.6
REMARK 620 3 CYS A 135 SG 115.2 115.1
REMARK 620 4 DDN A 308 O4 113.8 102.4 105.2
REMARK 620 N 1 2 3
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 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 702
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDN A 308
DBREF 1VQ2 A 1 193 UNP P16006 DCTD_BPT4 1 193
SEQADV 1VQ2 GLU A 115 UNP P16006 ARG 115 ENGINEERED MUTATION
SEQRES 1 A 193 MET LYS ALA SER THR VAL LEU GLN ILE ALA TYR LEU VAL
SEQRES 2 A 193 SER GLN GLU SER LYS CYS CYS SER TRP LYS VAL GLY ALA
SEQRES 3 A 193 VAL ILE GLU LYS ASN GLY ARG ILE ILE SER THR GLY TYR
SEQRES 4 A 193 ASN GLY SER PRO ALA GLY GLY VAL ASN CYS CYS ASP TYR
SEQRES 5 A 193 ALA ALA GLU GLN GLY TRP LEU LEU ASN LYS PRO LYS HIS
SEQRES 6 A 193 ALA ILE ILE GLN GLY HIS LYS PRO GLU CYS VAL SER PHE
SEQRES 7 A 193 GLY SER THR ASP ARG PHE VAL LEU ALA LYS GLU HIS ARG
SEQRES 8 A 193 SER ALA HIS SER GLU TRP SER SER LYS ASN GLU ILE HIS
SEQRES 9 A 193 ALA GLU LEU ASN ALA ILE LEU PHE ALA ALA GLU ASN GLY
SEQRES 10 A 193 SER SER ILE GLU GLY ALA THR MET TYR VAL THR LEU SER
SEQRES 11 A 193 PRO CYS PRO ASP CYS ALA LYS ALA ILE ALA GLN SER GLY
SEQRES 12 A 193 ILE LYS LYS LEU VAL TYR CYS GLU THR TYR ASP LYS ASN
SEQRES 13 A 193 LYS PRO GLY TRP ASP ASP ILE LEU ARG ASN ALA GLY ILE
SEQRES 14 A 193 GLU VAL PHE ASN VAL PRO LYS LYS ASN LEU ASN LYS LEU
SEQRES 15 A 193 ASN TRP GLU ASN ILE ASN GLU PHE CYS GLY GLU
HET ZN A 701 1
HET ZN A 702 1
HET DDN A 308 20
HETNAM ZN ZINC ION
HETNAM DDN 3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
HETSYN DDN ((2R,3S,5R)-3-HYDROXY-5-(4-HYDROXY-2-OXO-3,4-
HETSYN 2 DDN DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL
HETSYN 3 DDN DIHYDROGEN PHOSPHATE
FORMUL 2 ZN 2(ZN 2+)
FORMUL 4 DDN C9 H15 N2 O8 P
FORMUL 5 HOH *47(H2 O)
HELIX 1 1 LYS A 2 GLN A 15 1 14
HELIX 2 2 ASN A 48 GLY A 57 1 10
HELIX 3 3 HIS A 90 GLU A 102 1 13
HELIX 4 4 HIS A 104 GLY A 117 1 14
HELIX 5 5 CYS A 132 SER A 142 1 11
HELIX 6 6 ASP A 161 ALA A 167 1 7
HELIX 7 7 PRO A 175 LEU A 179 5 5
HELIX 8 8 ASN A 183 ILE A 187 5 5
SHEET 1 A 5 ARG A 33 TYR A 39 0
SHEET 2 A 5 GLY A 25 LYS A 30 -1 N ALA A 26 O GLY A 38
SHEET 3 A 5 THR A 124 LEU A 129 -1 O THR A 124 N GLU A 29
SHEET 4 A 5 LYS A 146 GLU A 151 1 O LYS A 146 N MET A 125
SHEET 5 A 5 GLU A 170 ASN A 173 1 O GLU A 170 N LEU A 147
SHEET 1 B 2 LEU A 59 LEU A 60 0
SHEET 2 B 2 VAL A 85 LEU A 86 -1 O VAL A 85 N LEU A 60
LINK SG CYS A 19 ZN ZN A 702 1555 1555 2.21
LINK SG CYS A 49 ZN ZN A 702 1555 1555 2.37
LINK NE2 HIS A 94 ZN ZN A 702 1555 1555 2.23
LINK OE2 GLU A 102 ZN ZN A 702 1555 1555 2.04
LINK ND1 HIS A 104 ZN ZN A 701 1555 1555 2.06
LINK SG CYS A 132 ZN ZN A 701 1555 1555 2.39
LINK SG CYS A 135 ZN ZN A 701 1555 1555 2.37
LINK O4 DDN A 308 ZN ZN A 701 1555 1555 2.22
SITE 1 AC1 4 HIS A 104 CYS A 132 CYS A 135 DDN A 308
SITE 1 AC2 4 CYS A 19 CYS A 49 HIS A 94 GLU A 102
SITE 1 AC3 19 CYS A 19 SER A 21 TRP A 22 VAL A 24
SITE 2 AC3 19 ASN A 40 ARG A 91 HIS A 94 SER A 95
SITE 3 AC3 19 SER A 98 GLU A 102 HIS A 104 ALA A 105
SITE 4 AC3 19 GLU A 106 PRO A 131 CYS A 132 CYS A 135
SITE 5 AC3 19 TYR A 153 LYS A 155 ZN A 701
CRYST1 114.528 114.528 76.950 90.00 90.00 120.00 P 63 2 2 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 0.008731 0.005041 0.000000 0.00000
SCALE2 0.000000 0.010082 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012995 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
