HEADER HYDROLASE 17-MAR-06 2CIC TITLE THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPASE TITLE 2 WITH SUBSTRATE ANALOGUE DUPNHPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMPYLOBACTER JEJUNI; SOURCE 3 ORGANISM_TAXID: 197; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGAND COMPLEX, HYDROLASE, DRUG TARGET, DUTP PYROPHOSPHATASE EXPDTA X-RAY DIFFRACTION AUTHOR O.V.MOROZ,M.HARKIOLAKI,D.GONZALEZ-PACANOWSKA,K.S.WILSON REVDAT 4 13-DEC-23 2CIC 1 REMARK LINK REVDAT 3 11-MAY-11 2CIC 1 KEYWDS JRNL REMARK FORMUL REVDAT 3 2 1 ATOM REVDAT 2 24-FEB-09 2CIC 1 VERSN REVDAT 1 27-MAR-07 2CIC 0 JRNL AUTH G.R.HEMSWORTH,O.V.MOROZ,M.J.FOGG,B.SCOTT,C.BOSCH-NAVARRETE, JRNL AUTH 2 D.GONZALEZ-PACANOWSKA,K.S.WILSON JRNL TITL THE CRYSTAL STRUCTURE OF THE LEISHMANIA MAJOR DEOXYURIDINE JRNL TITL 2 TRIPHOSPHATE NUCLEOTIDOHYDROLASE IN COMPLEX WITH NUCLEOTIDE JRNL TITL 3 ANALOGUES, DUMP, AND DEOXYURIDINE. JRNL REF J.BIOL.CHEM. V. 286 16470 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21454646 JRNL DOI 10.1074/JBC.M111.224873 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 31466 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1700 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1366 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 101 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1851 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 478 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -1.08000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.698 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1906 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1672 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2581 ; 1.928 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3911 ; 1.967 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 221 ; 5.544 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;36.784 ;25.938 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 349 ;13.984 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;16.907 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 282 ; 0.199 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2067 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 373 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 874 ; 0.349 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2116 ; 0.260 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 963 ; 0.196 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1053 ; 0.095 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 468 ; 0.331 ; 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): 39 ; 0.281 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 72 ; 0.285 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 69 ; 0.392 ; 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): 1442 ; 1.483 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1780 ; 1.842 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 971 ; 2.740 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 801 ; 3.786 ; 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 : NULL 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 2CIC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1290028218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33092 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1W2Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE PH 7.0, 20 MM REMARK 280 MAGNESIUM ACETATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-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 -1.000000 0.000000 0.000000 46.69850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 46.69850 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.81700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 46.69850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.90850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 46.69850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 107.72550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 46.69850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 107.72550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.69850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.90850 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 46.69850 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 46.69850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 71.81700 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 46.69850 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 46.69850 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 71.81700 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 46.69850 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 107.72550 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 46.69850 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 35.90850 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 46.69850 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 35.90850 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 46.69850 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 107.72550 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 46.69850 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 46.69850 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 71.81700 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: 6090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.4 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 0.000000 -1.000000 0.000000 93.39700 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 93.39700 REMARK 350 BIOMT3 2 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 ARG A 91 REMARK 465 ASP A 92 REMARK 465 LYS A 93 REMARK 465 ASN A 94 REMARK 465 ASN A 95 REMARK 465 LYS A 96 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TYR A 90 CG CD1 CD2 CE1 CE2 CZ OH REMARK 480 GLU A 104 CG CD OE1 OE2 REMARK 480 GLU A 117 CD OE1 OE2 REMARK 480 GLU A 210 CD OE1 OE2 REMARK 480 LYS A 220 CG CD CE NZ REMARK 480 LYS A 221 CD CE NZ REMARK 480 GLU A 224 CG CD OE1 OE2 REMARK 480 LYS A 227 CE NZ 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 HOH A 2042 O HOH A 2364 1.41 REMARK 500 O HOH A 2138 O HOH A 2143 1.60 REMARK 500 O HOH A 2353 O HOH A 2359 1.67 REMARK 500 CA GLY A 124 O HOH A 2288 1.72 REMARK 500 OG1 THR A 103 O HOH A 2243 1.77 REMARK 500 OE1 GLU A 224 O HOH A 2454 1.81 REMARK 500 O HOH A 2282 O HOH A 2295 1.85 REMARK 500 OE1 GLU A 117 O HOH A 2265 1.85 REMARK 500 O ILE A 6 O HOH A 2017 1.85 REMARK 500 O HOH A 2470 O HOH A 2475 1.86 REMARK 500 CB GLU A 104 O HOH A 2247 1.86 REMARK 500 C ALA A 229 O HOH A 2468 1.87 REMARK 500 O ASN A 146 O HOH A 2329 1.91 REMARK 500 O ARG A 182 O HOH A 2369 1.94 REMARK 500 CD GLU A 8 O HOH A 2023 1.95 REMARK 500 O HOH A 2300 O HOH A 2302 1.96 REMARK 500 O LEU A 36 O HOH A 2115 1.96 REMARK 500 O HOH A 2061 O HOH A 2062 1.96 REMARK 500 O HOH A 2170 O HOH A 2381 1.97 REMARK 500 O HOH A 2459 O HOH A 2460 1.97 REMARK 500 O ASN A 106 O HOH A 2251 2.00 REMARK 500 CD1 TYR A 90 O HOH A 2088 2.01 REMARK 500 O HOH A 2378 O HOH A 2379 2.01 REMARK 500 CB TYR A 127 O HOH A 2294 2.02 REMARK 500 N ASP A 214 O HOH A 2439 2.03 REMARK 500 OD1 ASN A 202 O HOH A 2418 2.03 REMARK 500 O HOH A 2076 O HOH A 2226 2.03 REMARK 500 OE2 GLU A 46 O HOH A 2135 2.03 REMARK 500 O HOH A 2124 O HOH A 2286 2.04 REMARK 500 O HOH A 2027 O HOH A 2035 2.04 REMARK 500 O GLU A 224 O HOH A 2455 2.04 REMARK 500 OE1 GLN A 207 O HOH A 2425 2.07 REMARK 500 CB TYR A 90 O HOH A 2234 2.07 REMARK 500 O HOH A 2438 O HOH A 2445 2.07 REMARK 500 OE1 GLU A 8 O HOH A 2023 2.08 REMARK 500 OE2 GLU A 8 O HOH A 2023 2.09 REMARK 500 O HOH A 2325 O HOH A 2326 2.09 REMARK 500 O TRP A 196 O HOH A 2396 2.09 REMARK 500 O HOH A 2022 O HOH A 2024 2.09 REMARK 500 O LYS A 227 O HOH A 2463 2.11 REMARK 500 O GLY A 198 O HOH A 2403 2.11 REMARK 500 O TYR A 226 O HOH A 2460 2.11 REMARK 500 O HOH A 2173 O HOH A 2377 2.12 REMARK 500 CD1 LEU A 178 O HOH A 2365 2.12 REMARK 500 N3A DUP A 1968 O HOH A 2477 2.12 REMARK 500 CG TYR A 90 O HOH A 2234 2.13 REMARK 500 N ASP A 52 O HOH A 2152 2.13 REMARK 500 O HOH A 2086 O HOH A 2233 2.14 REMARK 500 OE1 GLU A 123 O HOH A 2280 2.14 REMARK 500 O SER A 63 O HOH A 2179 2.14 REMARK 500 REMARK 500 THIS ENTRY HAS 62 CLOSE CONTACTS 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 HOH A 2288 O HOH A 2288 5554 1.72 REMARK 500 O HOH A 2143 O HOH A 2147 8665 1.80 REMARK 500 O HOH A 2113 O HOH A 2297 3655 1.93 REMARK 500 O HOH A 2282 O HOH A 2289 5554 1.94 REMARK 500 O HOH A 2312 O HOH A 2321 8665 1.95 REMARK 500 O HOH A 2125 O HOH A 2296 8665 2.06 REMARK 500 O HOH A 2096 O HOH A 2131 3655 2.06 REMARK 500 O HOH A 2163 O HOH A 2470 8665 2.07 REMARK 500 O HOH A 2279 O HOH A 2286 5554 2.09 REMARK 500 O HOH A 2070 O HOH A 2131 3655 2.10 REMARK 500 O HOH A 2428 O HOH A 2431 15555 2.12 REMARK 500 O HOH A 2279 O HOH A 2279 5554 2.16 REMARK 500 O HOH A 2168 O HOH A 2387 8665 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 TYR A 90 CB TYR A 90 CG -0.736 REMARK 500 GLU A 117 CG GLU A 117 CD 0.283 REMARK 500 GLU A 210 CG GLU A 210 CD -0.144 REMARK 500 LYS A 227 CD LYS A 227 CE -0.346 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 MET A 10 CG - SD - CE ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 THR A 55 CA - CB - CG2 ANGL. DEV. = 9.1 DEGREES REMARK 500 TYR A 90 CA - CB - CG ANGL. DEV. = 25.8 DEGREES REMARK 500 TYR A 90 CB - CG - CD2 ANGL. DEV. = 20.2 DEGREES REMARK 500 TYR A 90 CB - CG - CD1 ANGL. DEV. = -23.5 DEGREES REMARK 500 GLU A 117 CG - CD - OE1 ANGL. DEV. = -16.5 DEGREES REMARK 500 LYS A 221 CB - CG - CD ANGL. DEV. = 18.2 DEGREES REMARK 500 LYS A 227 CG - CD - CE ANGL. DEV. = 40.0 DEGREES REMARK 500 LYS A 227 CD - CE - NZ ANGL. DEV. = -15.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 90 0.09 SIDE CHAIN REMARK 500 GLU A 117 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2012 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH A2065 DISTANCE = 6.08 ANGSTROMS 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 A1969 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 46 OE2 REMARK 620 2 GLU A 46 OE1 46.0 REMARK 620 3 DUP A1968 O1A 111.4 147.2 REMARK 620 4 DUP A1968 O2B 104.5 81.4 83.9 REMARK 620 5 HOH A2161 O 84.6 109.6 86.9 169.0 REMARK 620 6 HOH A2470 O 149.0 126.3 85.5 102.9 70.1 REMARK 620 7 HOH A2475 O 126.5 89.4 120.6 93.0 86.4 37.5 REMARK 620 8 HOH A2477 O 164.2 130.4 63.3 60.9 109.2 46.7 63.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1970 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 46 OE1 REMARK 620 2 GLU A 74 OE2 85.1 REMARK 620 3 ASP A 77 OD2 94.4 96.3 REMARK 620 4 DUP A1968 O2B 99.2 159.8 102.9 REMARK 620 5 HOH A2213 O 152.4 82.0 63.1 101.3 REMARK 620 6 HOH A2469 O 144.9 88.7 120.7 76.4 59.3 REMARK 620 7 HOH A2472 O 94.1 69.9 163.1 90.1 104.2 51.6 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 MG A 1969 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1970 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUP A 1968 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1W2Y RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPASE REMARK 900 WITH SUBSTRATE ANALOGUE DUPNHP REMARK 900 RELATED ID: 2YAY RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX WITH REMARK 900 SUBSTRATE ANALOGUE DUPNPP REMARK 900 RELATED ID: 2CJE RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF A COMPLEX OF LEISHMANIA MAJOR DUTPASE WITH REMARK 900 SUBSTRATE ANALOGUE DUPNHP REMARK 900 RELATED ID: 2YAZ RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX DUMP REMARK 900 RELATED ID: 2YB0 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX REMARK 900 DEOXYURIDINE DBREF 2CIC A 1 229 UNP Q9PMK9 Q9PMK9_CAMJE 1 229 SEQRES 1 A 229 MET THR ASN ILE GLU ILE LEU GLU ASN MET LEU LYS LEU SEQRES 2 A 229 GLN GLN LYS LEU ASN ASP GLU THR ASN GLY LEU ASN TRP SEQRES 3 A 229 GLU ASN GLY TYR THR LYS GLU GLY LYS LEU ILE SER TRP SEQRES 4 A 229 ARG ARG CYS ILE TYR MET GLU CYS ALA GLU LEU ILE ASP SEQRES 5 A 229 SER PHE THR TRP LYS HIS TRP LYS ASN ILE SER SER LEU SEQRES 6 A 229 THR ASN TRP GLU ASN VAL ARG ILE GLU ILE VAL ASP ILE SEQRES 7 A 229 TRP HIS PHE ILE LEU SER LEU LEU LEU GLU GLU TYR ARG SEQRES 8 A 229 ASP LYS ASN ASN LYS ASP PHE LYS ALA ILE ALA THR GLU SEQRES 9 A 229 VAL ASN ALA VAL SER VAL PHE GLN ASP PHE CYS LYS GLU SEQRES 10 A 229 GLU GLU TYR PRO ASN GLU GLY ASP ILE TYR GLY ILE LEU SEQRES 11 A 229 ASN ASP ILE GLU LEU ILE ILE HIS LYS CYS SER GLY PHE SEQRES 12 A 229 GLY PHE ASN LEU GLY GLU LEU LEU SER THR TYR PHE THR SEQRES 13 A 229 LEU ALA ILE LYS CYS GLY LEU ASN LEU GLU ILE LEU TYR SEQRES 14 A 229 LYS THR TYR ILE GLY LYS ASN VAL LEU ASN ILE PHE ARG SEQRES 15 A 229 GLN ASN ASN GLY TYR LYS ASP GLY SER TYR LYS LYS THR SEQRES 16 A 229 TRP ASN GLY LYS GLU ASP ASN GLU VAL LEU ALA GLN ILE SEQRES 17 A 229 LEU GLU GLN GLU LEU ASP PHE ASP THR ILE TYR LYS LYS SEQRES 18 A 229 LEU GLU GLU CYS TYR LYS LYS ALA HET DUP A1968 28 HET MG A1969 1 HET MG A1970 1 HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 DUP C9 H16 N3 O13 P3 FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *478(H2 O) HELIX 1 1 THR A 2 GLY A 23 1 22 HELIX 2 2 ASN A 25 GLY A 29 5 5 HELIX 3 3 SER A 38 ASP A 52 1 15 HELIX 4 4 ASN A 67 TYR A 90 1 24 HELIX 5 5 ASP A 97 ALA A 107 1 11 HELIX 6 6 VAL A 108 CYS A 115 1 8 HELIX 7 7 ASN A 122 GLY A 124 5 3 HELIX 8 8 ASP A 125 GLY A 142 1 18 HELIX 9 9 ASN A 146 CYS A 161 1 16 HELIX 10 10 ASN A 164 ASN A 185 1 22 HELIX 11 11 ASP A 201 LEU A 209 1 9 HELIX 12 12 GLU A 210 GLU A 212 5 3 HELIX 13 13 ASP A 214 LYS A 227 1 14 SHEET 1 AA 2 THR A 195 TRP A 196 0 SHEET 2 AA 2 LYS A 199 GLU A 200 -1 O LYS A 199 N TRP A 196 LINK NZ LYS A 194 O2G DUP A1968 1555 1555 1.92 LINK OE2 GLU A 46 MG MG A1969 1555 1555 2.48 LINK OE1 GLU A 46 MG MG A1969 1555 1555 3.00 LINK OE1 GLU A 46 MG MG A1970 1555 1555 2.39 LINK OE2 GLU A 74 MG MG A1970 1555 1555 2.28 LINK OD2 ASP A 77 MG MG A1970 1555 1555 2.38 LINK O1A DUP A1968 MG MG A1969 1555 1555 2.41 LINK O2B DUP A1968 MG MG A1969 1555 1555 2.41 LINK O2B DUP A1968 MG MG A1970 1555 1555 2.27 LINK MG MG A1969 O HOH A2161 1555 8665 2.57 LINK MG MG A1969 O HOH A2470 1555 1555 3.04 LINK MG MG A1969 O HOH A2475 1555 1555 2.26 LINK MG MG A1969 O HOH A2477 1555 1555 2.69 LINK MG MG A1970 O HOH A2213 1555 1555 2.78 LINK MG MG A1970 O HOH A2469 1555 1555 2.60 LINK MG MG A1970 O HOH A2472 1555 1555 3.02 SITE 1 AC1 7 GLU A 46 DUP A1968 MG A1970 HOH A2161 SITE 2 AC1 7 HOH A2470 HOH A2475 HOH A2477 SITE 1 AC2 8 GLU A 46 GLU A 74 ASP A 77 DUP A1968 SITE 2 AC2 8 MG A1969 HOH A2213 HOH A2469 HOH A2472 SITE 1 AC3 34 GLN A 14 LEU A 17 ASN A 18 ASN A 22 SITE 2 AC3 34 TRP A 39 GLU A 46 LYS A 57 HIS A 58 SITE 3 AC3 34 TRP A 59 ASP A 77 HIS A 80 PHE A 81 SITE 4 AC3 34 LYS A 175 ASN A 179 ARG A 182 TYR A 187 SITE 5 AC3 34 LYS A 194 ASN A 202 MG A1969 MG A1970 SITE 6 AC3 34 HOH A2135 HOH A2366 HOH A2392 HOH A2415 SITE 7 AC3 34 HOH A2469 HOH A2470 HOH A2471 HOH A2472 SITE 8 AC3 34 HOH A2473 HOH A2474 HOH A2475 HOH A2476 SITE 9 AC3 34 HOH A2477 HOH A2478 CRYST1 93.397 93.397 143.634 90.00 90.00 90.00 I 41 2 2 16 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 0.010707 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006962 0.00000