HEADER HYDROLASE 31-AUG-06 2J4H TITLE CRYSTAL STRUCTURE OF A H121A ESCHERICHIA COLI DCTP DEAMINASE MUTANT TITLE 2 ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DCTP DEAMINASE; COMPND 5 EC: 3.5.4.13; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DCTP DEAMINASE, HYDROLASE, NUCLEOTIDE METABOLISM, TRIMER EXPDTA X-RAY DIFFRACTION AUTHOR E.JOHANSSON,M.THYMARK,J.H.BYNCK,M.FANOE,S.LARSEN,M.WILLEMOES REVDAT 6 08-MAY-24 2J4H 1 LINK REVDAT 5 06-MAR-19 2J4H 1 REMARK REVDAT 4 17-JAN-18 2J4H 1 REMARK REVDAT 3 24-FEB-09 2J4H 1 VERSN REVDAT 2 21-AUG-07 2J4H 1 JRNL REVDAT 1 07-AUG-07 2J4H 0 JRNL AUTH E.JOHANSSON,M.THYMARK,J.H.BYNCK,M.FANOE,S.LARSEN,M.WILLEMOES JRNL TITL REGULATION OF DCTP DEAMINASE FROM ESCHERICHIA COLI BY JRNL TITL 2 NONALLOSTERIC DTTP BINDING TO AN INACTIVE FORM OF THE ENZYME JRNL REF FEBS J. V. 274 4188 2007 JRNL REFN ISSN 1742-464X JRNL PMID 17651436 JRNL DOI 10.1111/J.1742-4658.2007.05945.X REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0001 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 10539 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 563 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 562 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 29 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2656 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.28000 REMARK 3 B22 (A**2) : 2.28000 REMARK 3 B33 (A**2) : -3.42000 REMARK 3 B12 (A**2) : 1.14000 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): 0.390 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.256 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.605 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.914 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2764 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2606 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3766 ; 1.579 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6008 ; 0.911 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 344 ; 6.884 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;36.765 ;22.241 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 438 ;16.542 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;22.129 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 422 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3066 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 578 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 499 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2510 ; 0.199 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1787 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 49 ; 0.070 ; 0.200 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): 48 ; 0.151 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 240 ; 0.224 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.240 ; 0.200 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): 2160 ; 0.956 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2760 ; 1.061 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1179 ; 1.303 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1006 ; 2.093 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 13 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 5 1 REMARK 3 1 B 1 B 5 1 REMARK 3 2 A 7 A 8 1 REMARK 3 2 B 7 B 8 1 REMARK 3 3 A 10 A 13 1 REMARK 3 3 B 10 B 13 1 REMARK 3 4 A 15 A 19 1 REMARK 3 4 B 15 B 19 1 REMARK 3 5 A 21 A 35 1 REMARK 3 5 B 21 B 35 1 REMARK 3 6 A 37 A 39 1 REMARK 3 6 B 37 B 39 1 REMARK 3 7 A 41 A 55 1 REMARK 3 7 B 41 B 55 1 REMARK 3 8 A 57 A 64 1 REMARK 3 8 B 57 B 64 1 REMARK 3 9 A 67 A 76 1 REMARK 3 9 B 67 B 76 1 REMARK 3 10 A 78 A 105 1 REMARK 3 10 B 78 B 105 1 REMARK 3 11 A 107 A 124 1 REMARK 3 11 B 107 B 124 1 REMARK 3 12 A 126 A 171 1 REMARK 3 12 B 126 B 171 1 REMARK 3 13 A 194 A 194 1 REMARK 3 13 B 194 B 194 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 2417 ; 0.03 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 2417 ; 0.10 ; 0.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 2J4H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1290029517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.046 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11131 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 94.2 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOUR DIFFUSION, 34% PEG400, 0.2M REMARK 280 MAGNESIUM CHLORIDE, 0.1M HEPES PH6.8, 5MM DCTP, VAPOR DIFFUSION 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 171.22200 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 171.22200 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 171.22200 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 171.22200 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 171.22200 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 171.22200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.7 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 0.00000 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 0.00000 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 62.54500 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 31.27250 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 -54.16556 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, HIS 121 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, HIS 121 TO ALA 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 175 REMARK 465 ASP A 176 REMARK 465 ALA A 177 REMARK 465 LYS A 178 REMARK 465 TYR A 179 REMARK 465 ARG A 180 REMARK 465 ASN A 181 REMARK 465 GLN A 182 REMARK 465 GLN A 183 REMARK 465 GLY A 184 REMARK 465 ALA A 185 REMARK 465 VAL A 186 REMARK 465 ALA A 187 REMARK 465 SER A 188 REMARK 465 ARG A 189 REMARK 465 ILE A 190 REMARK 465 ASP A 191 REMARK 465 LYS A 192 REMARK 465 ASP A 193 REMARK 465 ARG B 173 REMARK 465 ARG B 174 REMARK 465 GLU B 175 REMARK 465 ASP B 176 REMARK 465 ALA B 177 REMARK 465 LYS B 178 REMARK 465 TYR B 179 REMARK 465 ARG B 180 REMARK 465 ASN B 181 REMARK 465 GLN B 182 REMARK 465 GLN B 183 REMARK 465 GLY B 184 REMARK 465 ALA B 185 REMARK 465 VAL B 186 REMARK 465 ALA B 187 REMARK 465 SER B 188 REMARK 465 ARG B 189 REMARK 465 ILE B 190 REMARK 465 ASP B 191 REMARK 465 LYS B 192 REMARK 465 ASP B 193 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 7 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 34 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 126 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP B 34 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 66 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES 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 PRO A 57 167.27 -49.79 REMARK 500 SER A 70 174.04 -58.35 REMARK 500 GLU A 79 142.07 -32.53 REMARK 500 ALA A 121 90.73 -17.33 REMARK 500 VAL A 122 -71.21 90.58 REMARK 500 SER B 70 176.41 -55.46 REMARK 500 ASP B 76 -173.51 -69.86 REMARK 500 GLU B 79 141.68 -31.75 REMARK 500 ALA B 121 88.60 -16.46 REMARK 500 VAL B 122 -68.06 90.90 REMARK 500 ARG B 169 75.02 -119.44 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 MG A1177 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 121 O REMARK 620 2 VAL A 122 N 46.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1176 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 YYY A1175 O1A REMARK 620 2 YYY A1175 O1B 72.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1175 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 121 O REMARK 620 2 VAL B 122 N 48.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1174 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 YYY B1173 O1A REMARK 620 2 YYY B1173 O1B 74.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YYY A1175 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1176 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YYY B1173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1174 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1177 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1175 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XS1 RELATED DB: PDB REMARK 900 DCTP DEAMINASE FROM ESCHERICHIA COLI IN COMPLEX WITH DUTP REMARK 900 RELATED ID: 1XS4 RELATED DB: PDB REMARK 900 DCTP DEAMINASE FROM ESCHERICHIA COLI- E138A MUTANT ENZYMEIN COMPLEX REMARK 900 WITH DCTP REMARK 900 RELATED ID: 1XS6 RELATED DB: PDB REMARK 900 DCTP DEAMINASE FROM ESCHERICHIA COLI. E138A MUTANT ENZYMEIN COMPLEX REMARK 900 WITH DUTP REMARK 900 RELATED ID: 2J4Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A E138A ESCHERICHIA COLI DCTP DEAMINASE MUTANT REMARK 900 ENZYME IN COMPLEX WITH DTTP DBREF 2J4H A 1 193 UNP P28248 DCD_ECOLI 1 193 DBREF 2J4H B 1 193 UNP P28248 DCD_ECOLI 1 193 SEQADV 2J4H ALA A 121 UNP P28248 HIS 121 ENGINEERED MUTATION SEQADV 2J4H ALA B 121 UNP P28248 HIS 121 ENGINEERED MUTATION SEQRES 1 A 193 MET ARG LEU CYS ASP ARG ASP ILE GLU ALA TRP LEU ASP SEQRES 2 A 193 GLU GLY ARG LEU SER ILE ASN PRO ARG PRO PRO VAL GLU SEQRES 3 A 193 ARG ILE ASN GLY ALA THR VAL ASP VAL ARG LEU GLY ASN SEQRES 4 A 193 LYS PHE ARG THR PHE ARG GLY HIS THR ALA ALA PHE ILE SEQRES 5 A 193 ASP LEU SER GLY PRO LYS ASP GLU VAL SER ALA ALA LEU SEQRES 6 A 193 ASP ARG VAL MET SER ASP GLU ILE VAL LEU ASP GLU GLY SEQRES 7 A 193 GLU ALA PHE TYR LEU HIS PRO GLY GLU LEU ALA LEU ALA SEQRES 8 A 193 VAL THR LEU GLU SER VAL THR LEU PRO ALA ASP LEU VAL SEQRES 9 A 193 GLY TRP LEU ASP GLY ARG SER SER LEU ALA ARG LEU GLY SEQRES 10 A 193 LEU MET VAL ALA VAL THR ALA HIS ARG ILE ASP PRO GLY SEQRES 11 A 193 TRP SER GLY CYS ILE VAL LEU GLU PHE TYR ASN SER GLY SEQRES 12 A 193 LYS LEU PRO LEU ALA LEU ARG PRO GLY MET LEU ILE GLY SEQRES 13 A 193 ALA LEU SER PHE GLU PRO LEU SER GLY PRO ALA VAL ARG SEQRES 14 A 193 PRO TYR ASN ARG ARG GLU ASP ALA LYS TYR ARG ASN GLN SEQRES 15 A 193 GLN GLY ALA VAL ALA SER ARG ILE ASP LYS ASP SEQRES 1 B 193 MET ARG LEU CYS ASP ARG ASP ILE GLU ALA TRP LEU ASP SEQRES 2 B 193 GLU GLY ARG LEU SER ILE ASN PRO ARG PRO PRO VAL GLU SEQRES 3 B 193 ARG ILE ASN GLY ALA THR VAL ASP VAL ARG LEU GLY ASN SEQRES 4 B 193 LYS PHE ARG THR PHE ARG GLY HIS THR ALA ALA PHE ILE SEQRES 5 B 193 ASP LEU SER GLY PRO LYS ASP GLU VAL SER ALA ALA LEU SEQRES 6 B 193 ASP ARG VAL MET SER ASP GLU ILE VAL LEU ASP GLU GLY SEQRES 7 B 193 GLU ALA PHE TYR LEU HIS PRO GLY GLU LEU ALA LEU ALA SEQRES 8 B 193 VAL THR LEU GLU SER VAL THR LEU PRO ALA ASP LEU VAL SEQRES 9 B 193 GLY TRP LEU ASP GLY ARG SER SER LEU ALA ARG LEU GLY SEQRES 10 B 193 LEU MET VAL ALA VAL THR ALA HIS ARG ILE ASP PRO GLY SEQRES 11 B 193 TRP SER GLY CYS ILE VAL LEU GLU PHE TYR ASN SER GLY SEQRES 12 B 193 LYS LEU PRO LEU ALA LEU ARG PRO GLY MET LEU ILE GLY SEQRES 13 B 193 ALA LEU SER PHE GLU PRO LEU SER GLY PRO ALA VAL ARG SEQRES 14 B 193 PRO TYR ASN ARG ARG GLU ASP ALA LYS TYR ARG ASN GLN SEQRES 15 B 193 GLN GLY ALA VAL ALA SER ARG ILE ASP LYS ASP HET YYY A1175 24 HET MG A1176 1 HET MG A1177 1 HET YYY B1173 24 HET MG B1174 1 HET MG B1175 1 HETNAM YYY DEOXYCYTIDINE DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 YYY 2(C9 H15 N3 O10 P2) FORMUL 4 MG 4(MG 2+) HELIX 1 1 CYS A 4 GLU A 14 1 11 HELIX 2 2 PRO A 24 GLU A 26 5 3 HELIX 3 3 ARG A 45 ALA A 49 5 5 HELIX 4 4 PRO A 57 MET A 69 1 13 HELIX 5 5 ARG A 110 ARG A 115 1 6 HELIX 6 6 CYS B 4 GLU B 14 1 11 HELIX 7 7 PRO B 24 GLU B 26 5 3 HELIX 8 8 ARG B 45 ALA B 49 5 5 HELIX 9 9 PRO B 57 MET B 69 1 13 HELIX 10 10 ARG B 110 ARG B 115 1 6 SHEET 1 AA 4 SER A 18 ASN A 20 0 SHEET 2 AA 4 LEU A 88 THR A 98 -1 O SER A 96 N ASN A 20 SHEET 3 AA 4 SER A 132 ASN A 141 -1 O GLY A 133 N VAL A 97 SHEET 4 AA 4 LEU A 118 VAL A 120 -1 O MET A 119 N TYR A 140 SHEET 1 AB 5 ILE A 28 ASN A 29 0 SHEET 2 AB 5 THR A 32 ARG A 36 -1 O THR A 32 N ASN A 29 SHEET 3 AB 5 LEU A 154 PRO A 162 -1 N ILE A 155 O VAL A 35 SHEET 4 AB 5 LEU A 103 GLY A 109 -1 O VAL A 104 N GLU A 161 SHEET 5 AB 5 ARG A 126 ILE A 127 -1 O ILE A 127 N GLY A 105 SHEET 1 AC 2 LYS A 40 PHE A 41 0 SHEET 2 AC 2 ILE A 73 VAL A 74 -1 O ILE A 73 N PHE A 41 SHEET 1 AD 2 PHE A 81 LEU A 83 0 SHEET 2 AD 2 LEU A 147 LEU A 149 -1 O LEU A 147 N LEU A 83 SHEET 1 BA 4 SER B 18 ASN B 20 0 SHEET 2 BA 4 LEU B 88 THR B 98 -1 O SER B 96 N ASN B 20 SHEET 3 BA 4 SER B 132 ASN B 141 -1 O GLY B 133 N VAL B 97 SHEET 4 BA 4 LEU B 118 VAL B 120 -1 O MET B 119 N TYR B 140 SHEET 1 BB 5 ILE B 28 ASN B 29 0 SHEET 2 BB 5 THR B 32 ARG B 36 -1 O THR B 32 N ASN B 29 SHEET 3 BB 5 LEU B 154 PRO B 162 -1 N ILE B 155 O VAL B 35 SHEET 4 BB 5 LEU B 103 GLY B 109 -1 O VAL B 104 N GLU B 161 SHEET 5 BB 5 ARG B 126 ILE B 127 -1 O ILE B 127 N GLY B 105 SHEET 1 BC 2 LYS B 40 PHE B 41 0 SHEET 2 BC 2 ILE B 73 VAL B 74 -1 O ILE B 73 N PHE B 41 SHEET 1 BD 2 PHE B 81 LEU B 83 0 SHEET 2 BD 2 LEU B 147 LEU B 149 -1 O LEU B 147 N LEU B 83 LINK O ALA A 121 MG MG A1177 1555 1555 2.82 LINK N VAL A 122 MG MG A1177 1555 1555 2.82 LINK O1A YYY A1175 MG MG A1176 1555 1555 2.20 LINK O1B YYY A1175 MG MG A1176 1555 1555 2.49 LINK O ALA B 121 MG MG B1175 1555 1555 2.43 LINK N VAL B 122 MG MG B1175 1555 1555 2.81 LINK O1A YYY B1173 MG MG B1174 1555 1555 2.00 LINK O1B YYY B1173 MG MG B1174 1555 1555 2.47 CISPEP 1 ASN A 20 PRO A 21 0 -1.93 CISPEP 2 ALA A 121 VAL A 122 0 13.67 CISPEP 3 ASN B 20 PRO B 21 0 -5.91 CISPEP 4 ALA B 121 VAL B 122 0 15.28 SITE 1 AC1 14 GLY A 109 ARG A 110 SER A 111 SER A 112 SITE 2 AC1 14 ARG A 115 ALA A 121 ALA A 124 ARG A 126 SITE 3 AC1 14 ASP A 128 TRP A 131 ILE A 135 VAL A 136 SITE 4 AC1 14 GLU A 138 MG A1176 SITE 1 AC2 1 YYY A1175 SITE 1 AC3 14 GLY B 109 ARG B 110 SER B 111 SER B 112 SITE 2 AC3 14 ARG B 115 ALA B 121 ALA B 124 ARG B 126 SITE 3 AC3 14 ASP B 128 TRP B 131 ILE B 135 VAL B 136 SITE 4 AC3 14 GLU B 138 MG B1174 SITE 1 AC4 1 YYY B1173 SITE 1 AC5 3 ALA A 121 VAL A 122 HIS A 125 SITE 1 AC6 4 LEU B 107 ALA B 121 VAL B 122 HIS B 125 CRYST1 62.545 62.545 342.444 90.00 90.00 120.00 P 63 2 2 24 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015988 0.009231 0.000000 0.00000 SCALE2 0.000000 0.018462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002920 0.00000 MTRIX1 1 -0.873800 0.486300 0.000542 36.05000 1 MTRIX2 1 0.486300 0.873800 -0.007390 1.06100 1 MTRIX3 1 -0.004067 0.006193 -1.000000 85.71000 1