HEADER HYDROLASE 05-SEP-06 2J4Q TITLE CRYSTAL STRUCTURE OF A E138A ESCHERICHIA COLI DCTP DEAMINASE MUTANT TITLE 2 ENZYME IN COMPLEX WITH DTTP 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 NUCLEOTIDE METABOLISM, TRIMER, HYDROLASE, DCTP DEAMINASE EXPDTA X-RAY DIFFRACTION AUTHOR E.JOHANSSON,M.THYMARK,J.H.BYNCK,M.FANOE,S.LARSEN,M.WILLEMOES REVDAT 7 13-DEC-23 2J4Q 1 REMARK LINK REVDAT 6 06-MAR-19 2J4Q 1 REMARK REVDAT 5 17-JAN-18 2J4Q 1 REMARK REVDAT 4 24-FEB-09 2J4Q 1 VERSN REVDAT 3 15-APR-08 2J4Q 1 REMARK FORMUL ATOM HETATM REVDAT 3 2 1 MASTER REVDAT 2 21-AUG-07 2J4Q 1 JRNL REVDAT 1 07-AUG-07 2J4Q 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. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 11438 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) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 582 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 591 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 27 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2641 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 5 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.26000 REMARK 3 B22 (A**2) : 2.26000 REMARK 3 B33 (A**2) : -3.38000 REMARK 3 B12 (A**2) : 1.13000 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): 1.388 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.398 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.265 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.067 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.893 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.871 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2755 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2579 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3756 ; 1.716 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5941 ; 1.027 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 343 ; 7.543 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;35.017 ;22.018 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 434 ;18.017 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;23.781 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 421 ; 0.242 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3037 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 564 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 508 ; 0.227 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2548 ; 0.197 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1727 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 68 ; 0.149 ; 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): 70 ; 0.218 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 291 ; 0.209 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.199 ; 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): 2170 ; 1.082 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2751 ; 1.220 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1179 ; 1.666 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1005 ; 2.524 ; 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 : 11 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 53 1 REMARK 3 7 B 41 B 53 1 REMARK 3 8 A 67 A 76 1 REMARK 3 8 B 67 B 76 1 REMARK 3 9 A 78 A 105 1 REMARK 3 9 B 78 B 105 1 REMARK 3 10 A 107 A 120 1 REMARK 3 10 B 107 B 120 1 REMARK 3 11 A 126 A 171 1 REMARK 3 11 B 126 B 171 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 2193 ; 0.04 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 2193 ; 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 2J4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1290029869. 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 : 12085 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 92.7 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1XS1 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 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 172.38300 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 172.38300 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 172.38300 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 172.38300 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 172.38300 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 172.38300 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.1 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.1 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 61.59400 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 30.79700 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 -53.34197 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2002 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2003 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 138 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, GLU 138 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 ASN B 172 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 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 TRP B 106 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 106 CZ3 CH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HIS B 121 O HOH B 2001 1.60 REMARK 500 CG2 THR B 123 O HOH B 2002 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 122 CG2 VAL A 122 3555 1.77 REMARK 500 O VAL B 122 CG2 VAL B 122 2545 1.99 REMARK 500 OD2 ASP B 7 OG SER B 164 3655 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 14 CG GLU A 14 CD 0.092 REMARK 500 REMARK 500 REMARK: NULL 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. = 7.7 DEGREES REMARK 500 ASP A 102 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP B 53 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 71 CB - CG - OD2 ANGL. DEV. = 6.2 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 57 103.18 -56.58 REMARK 500 ASP A 59 -80.08 -50.68 REMARK 500 GLU A 77 134.77 -21.69 REMARK 500 LEU A 118 99.17 -66.35 REMARK 500 HIS A 121 104.36 19.54 REMARK 500 VAL A 122 -11.74 -164.97 REMARK 500 LEU B 54 -77.37 -66.56 REMARK 500 SER B 55 133.31 -29.46 REMARK 500 ALA B 64 56.63 -104.51 REMARK 500 LEU B 65 31.31 -141.08 REMARK 500 GLU B 77 152.49 -45.36 REMARK 500 HIS B 121 122.79 -2.20 REMARK 500 VAL B 122 -21.72 -176.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 121 VAL A 122 -138.28 REMARK 500 HIS B 121 VAL B 122 -125.10 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 B 195 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TTP B 194 O2A REMARK 620 2 TTP B 194 O1G 75.9 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 TYD A 194 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP B 194 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 195 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: 2J4H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A H121A ESCHERICHIA COLI DCTP DEAMINASE MUTANT REMARK 900 ENZYME DBREF 2J4Q A 1 193 UNP P28248 DCD_ECOLI 1 193 DBREF 2J4Q B 1 193 UNP P28248 DCD_ECOLI 1 193 SEQADV 2J4Q ALA A 138 UNP P28248 GLU 138 ENGINEERED MUTATION SEQADV 2J4Q ALA B 138 UNP P28248 GLU 138 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 HIS VAL THR ALA HIS ARG ILE ASP PRO GLY SEQRES 11 A 193 TRP SER GLY CYS ILE VAL LEU ALA 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 HIS VAL THR ALA HIS ARG ILE ASP PRO GLY SEQRES 11 B 193 TRP SER GLY CYS ILE VAL LEU ALA 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 TYD A 194 25 HET TTP B 194 29 HET MG B 195 1 HETNAM TYD THYMIDINE-5'-DIPHOSPHATE HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 TYD C10 H16 N2 O11 P2 FORMUL 4 TTP C10 H17 N2 O14 P3 FORMUL 5 MG MG 2+ FORMUL 6 HOH *5(H2 O) 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 ALA B 64 1 8 HELIX 10 10 ARG B 110 ARG B 115 1 6 SHEET 1 AA 3 SER A 18 ASN A 20 0 SHEET 2 AA 3 SER A 96 THR A 98 -1 O SER A 96 N ASN A 20 SHEET 3 AA 3 SER A 132 GLY A 133 -1 O GLY A 133 N VAL A 97 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 ASP A 108 -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 AE 3 LEU A 88 VAL A 92 0 SHEET 2 AE 3 VAL A 136 ASN A 141 -1 O LEU A 137 N ALA A 91 SHEET 3 AE 3 LEU A 118 VAL A 120 -1 O MET A 119 N TYR A 140 SHEET 1 BA 3 SER B 18 ASN B 20 0 SHEET 2 BA 3 SER B 96 THR B 98 -1 O SER B 96 N ASN B 20 SHEET 3 BA 3 SER B 132 GLY B 133 -1 O GLY B 133 N VAL B 97 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 PHE B 81 LEU B 83 0 SHEET 2 BC 2 LEU B 147 LEU B 149 -1 O LEU B 147 N LEU B 83 SHEET 1 BD 3 LEU B 88 VAL B 92 0 SHEET 2 BD 3 VAL B 136 ASN B 141 -1 O LEU B 137 N ALA B 91 SHEET 3 BD 3 LEU B 118 VAL B 120 -1 O MET B 119 N TYR B 140 LINK O2A TTP B 194 MG MG B 195 1555 1555 2.78 LINK O1G TTP B 194 MG MG B 195 1555 1555 2.50 CISPEP 1 ASN A 20 PRO A 21 0 -0.38 CISPEP 2 ASN B 20 PRO B 21 0 0.55 SITE 1 AC1 11 ARG A 110 SER A 111 SER A 112 ARG A 115 SITE 2 AC1 11 HIS A 121 ALA A 124 ARG A 126 ASP A 128 SITE 3 AC1 11 ILE A 135 VAL A 136 TYR A 171 SITE 1 AC2 13 ASP B 34 ARG B 110 SER B 111 SER B 112 SITE 2 AC2 13 ARG B 115 HIS B 121 ALA B 124 HIS B 125 SITE 3 AC2 13 ARG B 126 ASP B 128 ILE B 135 VAL B 136 SITE 4 AC2 13 MG B 195 SITE 1 AC3 4 GLY B 109 ARG B 126 ALA B 157 TTP B 194 CRYST1 61.594 61.594 344.766 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 0.016235 0.009373 0.000000 0.00000 SCALE2 0.000000 0.018747 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002901 0.00000