HEADER HYDROLASE 31-MAR-06 2CJE TITLE THE CRYSTAL STRUCTURE OF A COMPLEX OF LEISHMANIA MAJOR DUTPASE WITH TITLE 2 SUBSTRATE ANALOGUE DUPNHP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUTPASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEOXYURIDINE TRIPHOSPHATASE, DUTP DIPHOSPHATASE, DUTP COMPND 5 PYROPHOSPHATASE; COMPND 6 EC: 3.6.1.23; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-YSBLIC KEYWDS PATHOGEN, ALL-ALPHA, HYDROLASE, DRUG TARGET EXPDTA X-RAY DIFFRACTION AUTHOR O.V.MOROZ,M.J.FOGG,D.GONZALEZ-PACANOWSKA,K.S.WILSON REVDAT 5 13-DEC-23 2CJE 1 REMARK HETSYN LINK REVDAT 4 03-AUG-11 2CJE 1 JRNL REMARK REVDAT 3 13-JUL-11 2CJE 1 VERSN REVDAT 2 24-FEB-09 2CJE 1 VERSN REVDAT 1 17-APR-07 2CJE 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. 2.34 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) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 13849 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 737 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) : 2.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 970 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2000 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.01000 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): 0.278 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.812 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2082 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1824 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2846 ; 1.497 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4214 ; 0.939 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 259 ; 6.074 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 97 ;37.765 ;24.742 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 315 ;17.212 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;19.711 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 316 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2354 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 429 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 510 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1857 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1009 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1115 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 72 ; 0.170 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.015 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 10 ; 0.092 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 40 ; 0.294 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.128 ; 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): 1318 ; 0.669 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 518 ; 0.140 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2071 ; 1.096 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 886 ; 1.665 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 775 ; 2.509 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 44 REMARK 3 ORIGIN FOR THE GROUP (A): -2.7721 30.8726 1.7794 REMARK 3 T TENSOR REMARK 3 T11: -0.2826 T22: -0.0625 REMARK 3 T33: -0.1346 T12: -0.0196 REMARK 3 T13: -0.0078 T23: 0.1795 REMARK 3 L TENSOR REMARK 3 L11: 4.6009 L22: 2.4989 REMARK 3 L33: 8.2089 L12: -1.4059 REMARK 3 L13: -0.6284 L23: -2.3420 REMARK 3 S TENSOR REMARK 3 S11: -0.1347 S12: -0.4261 S13: -0.4120 REMARK 3 S21: 0.1857 S22: 0.0490 S23: -0.1450 REMARK 3 S31: 0.3928 S32: 0.5698 S33: 0.0857 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 45 A 170 REMARK 3 ORIGIN FOR THE GROUP (A): -8.4993 47.2182 -2.2091 REMARK 3 T TENSOR REMARK 3 T11: -0.1322 T22: -0.1025 REMARK 3 T33: -0.2140 T12: -0.0748 REMARK 3 T13: -0.0693 T23: 0.0832 REMARK 3 L TENSOR REMARK 3 L11: 2.8319 L22: 3.9022 REMARK 3 L33: 2.0802 L12: -1.4987 REMARK 3 L13: 0.8228 L23: -1.5921 REMARK 3 S TENSOR REMARK 3 S11: -0.2687 S12: -0.3160 S13: 0.3028 REMARK 3 S21: 0.5429 S22: 0.0613 S23: -0.2222 REMARK 3 S31: -0.4770 S32: 0.1068 S33: 0.2073 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 171 A 250 REMARK 3 ORIGIN FOR THE GROUP (A): -18.1505 28.8685 7.1760 REMARK 3 T TENSOR REMARK 3 T11: -0.2398 T22: -0.0059 REMARK 3 T33: -0.0438 T12: -0.0049 REMARK 3 T13: 0.0723 T23: 0.2549 REMARK 3 L TENSOR REMARK 3 L11: 5.4293 L22: 6.2112 REMARK 3 L33: 5.5458 L12: 0.8583 REMARK 3 L13: -0.1782 L23: 0.1593 REMARK 3 S TENSOR REMARK 3 S11: -0.1750 S12: -0.4419 S13: -0.4364 REMARK 3 S21: 0.4123 S22: 0.1667 S23: 0.5597 REMARK 3 S31: 0.2207 S32: -0.3318 S33: 0.0083 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 2CJE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1290028374. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-SEP-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.974 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14713 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 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 1OGK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3350 MME, 0.2 M MGCL2, 0.1M REMARK 280 BIS-TRIS PH 5.5, PH 5.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 97.68733 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 48.84367 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 73.26550 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 24.42183 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 122.10917 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 97.68733 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 48.84367 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 24.42183 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 73.26550 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 122.10917 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: PQS 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 -43.93300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 76.09419 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -24.42183 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 ARG A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 SER A 6 REMARK 465 ALA A 7 REMARK 465 ILE A 266 REMARK 465 LYS A 267 REMARK 465 ALA A 268 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 ASN A 8 CG OD1 ND2 REMARK 470 LEU A 14 CD1 CD2 REMARK 470 HIS A 15 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 105 CD CE NZ REMARK 470 LYS A 108 CG CD CE NZ REMARK 470 LYS A 118 CG CD CE NZ REMARK 470 GLU A 119 CG CD OE1 OE2 REMARK 470 ASN A 201 CB CG OD1 ND2 REMARK 470 LYS A 214 CB CG CD CE NZ REMARK 470 VAL A 216 CG1 CG2 REMARK 470 LEU A 218 CB CG CD1 CD2 REMARK 470 ASP A 219 CG OD1 OD2 REMARK 470 LYS A 226 CG CD CE NZ REMARK 470 GLN A 229 CG CD OE1 NE2 REMARK 470 LYS A 245 CE NZ REMARK 470 LEU A 258 CD1 CD2 REMARK 470 LYS A 260 CG CD CE NZ REMARK 470 ALA A 265 CB 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 240 CD GLU A 240 OE1 0.074 REMARK 500 GLU A 246 CD GLU A 246 OE1 0.081 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 ARG A 186 NE - CZ - NH1 ANGL. DEV. = 3.7 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 SER A 31 62.02 -113.16 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 A1267 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 48 OE2 REMARK 620 2 GLU A 51 OE1 88.0 REMARK 620 3 DUN A1266 O1A 92.3 173.1 REMARK 620 4 DUN A1266 O2B 90.3 98.0 88.9 REMARK 620 5 HOH A2015 O 172.4 84.6 94.9 92.4 REMARK 620 6 HOH A2016 O 84.0 82.8 90.3 174.2 93.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1268 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 48 OE1 REMARK 620 2 GLU A 51 OE2 87.2 REMARK 620 3 GLU A 76 OE1 93.8 81.9 REMARK 620 4 ASP A 79 OD2 99.6 172.5 94.6 REMARK 620 5 DUN A1266 O2B 98.9 79.6 156.9 102.1 REMARK 620 6 HOH A2086 O 166.4 79.4 81.6 93.6 81.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1269 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 51 OE2 REMARK 620 2 GLU A 76 OE2 90.8 REMARK 620 3 HOH A2030 O 158.2 81.6 REMARK 620 4 HOH A2033 O 104.7 101.5 96.8 REMARK 620 5 HOH A2086 O 77.4 78.7 81.0 177.8 REMARK 620 6 HOH A2088 O 79.5 160.0 101.0 97.9 82.1 REMARK 620 N 1 2 3 4 5 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 1267 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1268 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1269 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUN A 1266 REMARK 900 REMARK 900 RELATED ENTRIES 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: 2YB0 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX REMARK 900 DEOXYURIDINE REMARK 900 RELATED ID: 2YAZ RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX DUMP REMARK 900 RELATED ID: 2CIC RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPASE REMARK 900 WITH SUBSTRATE ANALOGUE DUPNHPP DBREF 2CJE A 1 268 UNP O15826 O15826_LEIMA 1 268 SEQRES 1 A 268 MET LYS ARG ALA ARG SER ALA ASN ILE PRO GLY ALA ILE SEQRES 2 A 268 LEU HIS SER LEU ALA GLU LEU GLN ASP GLY LEU ASN ALA SEQRES 3 A 268 MET ILE ASP PRO SER TRP ARG ALA VAL ARG SER LEU ASP SEQRES 4 A 268 ASN TRP ALA LEU ALA ILE THR MET GLU SER THR GLU LEU SEQRES 5 A 268 LEU ASP SER TYR PRO TRP LYS TRP TRP LYS ASN LEU ASN SEQRES 6 A 268 ALA THR PRO ASP LEU ALA ASN VAL ARG ILE GLU LEU VAL SEQRES 7 A 268 ASP ILE PHE HIS PHE SER LEU SER GLY ALA MET GLN MET SEQRES 8 A 268 ARG SER THR PRO ASP ASP GLU ILE PRO ALA ALA SER LEU SEQRES 9 A 268 LYS PRO LEU LYS GLU VAL MET THR THR PHE LEU PRO ALA SEQRES 10 A 268 LYS GLU CYS THR SER ASP PRO TYR GLY PHE VAL PHE PHE SEQRES 11 A 268 PRO LEU THR ASP THR GLN ASN ALA ILE ALA SER PHE ARG SEQRES 12 A 268 ASN ILE ILE GLN LEU ALA ASN ALA TYR ARG PHE ASP VAL SEQRES 13 A 268 ILE ILE GLU CYS ILE ILE TYR ALA ALA GLU ASP LEU GLY SEQRES 14 A 268 PHE ASN LEU VAL ALA TYR TYR ILE ALA LYS HIS THR LEU SEQRES 15 A 268 ASN CYS ILE ARG GLN LEU SER GLY TYR LYS ASP GLY SER SEQRES 16 A 268 TYR VAL LYS VAL ASN ASN GLY VAL GLU ASP ASN SER LEU SEQRES 17 A 268 LEU HIS ASN CYS ILE LYS ASP VAL SER LEU ASP GLU VAL SEQRES 18 A 268 LEU ASP ALA ASP LYS TYR VAL GLN ALA TRP ASN SER ILE SEQRES 19 A 268 MET ALA ASN VAL TYR GLU ALA PHE GLN ILE LYS GLU SER SEQRES 20 A 268 ASP ARG LYS ASP ALA GLU ARG TRP PHE ALA LEU ALA LYS SEQRES 21 A 268 GLU ASN ARG LEU ALA ILE LYS ALA HET DUN A1266 24 HET MG A1267 1 HET MG A1268 1 HET MG A1269 1 HETNAM DUN 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN DUN 2,4(1H,3H)-PYRIMIDINEDIONE; 1-[2-DEOXY-5-O- HETSYN 2 DUN [HYDROXY(PHOSPHONOAMINO)PHOSPHINYL]-BETA-D-ERYTHRO- HETSYN 3 DUN PENTOFURANOSYL]- FORMUL 2 DUN C9 H15 N3 O10 P2 FORMUL 3 MG 3(MG 2+) FORMUL 6 HOH *88(H2 O) HELIX 1 1 PRO A 10 ASP A 29 1 20 HELIX 2 2 SER A 31 ARG A 36 1 6 HELIX 3 3 SER A 37 ASP A 54 1 18 HELIX 4 4 ASP A 69 THR A 94 1 26 HELIX 5 5 PRO A 95 ILE A 99 5 5 HELIX 6 6 PRO A 100 LEU A 104 5 5 HELIX 7 7 PRO A 106 VAL A 110 5 5 HELIX 8 8 ASP A 134 ALA A 151 1 18 HELIX 9 9 ARG A 153 GLY A 169 1 17 HELIX 10 10 ASN A 171 SER A 189 1 19 HELIX 11 11 LEU A 208 ILE A 213 1 6 HELIX 12 12 SER A 217 ASP A 223 1 7 HELIX 13 13 LYS A 226 PHE A 242 1 17 HELIX 14 14 LYS A 245 ARG A 249 5 5 HELIX 15 15 ASP A 251 ASN A 262 1 12 SHEET 1 AA 2 THR A 121 SER A 122 0 SHEET 2 AA 2 PHE A 129 PHE A 130 -1 O PHE A 130 N THR A 121 SHEET 1 AB 2 VAL A 199 ASN A 200 0 SHEET 2 AB 2 VAL A 203 GLU A 204 -1 O VAL A 203 N ASN A 200 LINK OE2 GLU A 48 MG MG A1267 1555 1555 2.28 LINK OE1 GLU A 48 MG MG A1268 1555 1555 2.13 LINK OE1 GLU A 51 MG MG A1267 1555 1555 2.04 LINK OE2 GLU A 51 MG MG A1268 1555 1555 2.33 LINK OE2 GLU A 51 MG MG A1269 1555 1555 2.25 LINK OE1 GLU A 76 MG MG A1268 1555 1555 2.07 LINK OE2 GLU A 76 MG MG A1269 1555 1555 2.16 LINK OD2 ASP A 79 MG MG A1268 1555 1555 1.99 LINK O1A DUN A1266 MG MG A1267 1555 1555 1.97 LINK O2B DUN A1266 MG MG A1267 1555 1555 2.28 LINK O2B DUN A1266 MG MG A1268 1555 1555 2.17 LINK MG MG A1267 O HOH A2015 1555 1555 2.11 LINK MG MG A1267 O HOH A2016 1555 1555 2.16 LINK MG MG A1268 O HOH A2086 1555 1555 2.33 LINK MG MG A1269 O HOH A2030 1555 1555 2.35 LINK MG MG A1269 O HOH A2033 1555 1555 2.03 LINK MG MG A1269 O HOH A2086 1555 1555 2.50 LINK MG MG A1269 O HOH A2088 1555 1555 2.07 CISPEP 1 PHE A 130 PRO A 131 0 -1.29 SITE 1 AC1 6 GLU A 48 GLU A 51 DUN A1266 MG A1268 SITE 2 AC1 6 HOH A2015 HOH A2016 SITE 1 AC2 8 GLU A 48 GLU A 51 GLU A 76 ASP A 79 SITE 2 AC2 8 DUN A1266 MG A1267 MG A1269 HOH A2086 SITE 1 AC3 7 GLU A 51 GLU A 76 MG A1268 HOH A2030 SITE 2 AC3 7 HOH A2033 HOH A2086 HOH A2088 SITE 1 AC4 27 GLN A 21 LEU A 24 ASN A 25 ILE A 28 SITE 2 AC4 27 TRP A 41 GLU A 48 GLU A 51 LYS A 59 SITE 3 AC4 27 TRP A 60 TRP A 61 ASP A 79 HIS A 82 SITE 4 AC4 27 PHE A 83 LYS A 179 ASN A 183 ARG A 186 SITE 5 AC4 27 TYR A 191 LYS A 198 ASN A 206 MG A1267 SITE 6 AC4 27 MG A1268 HOH A2015 HOH A2016 HOH A2069 SITE 7 AC4 27 HOH A2086 HOH A2087 HOH A2088 CRYST1 87.866 87.866 146.531 90.00 90.00 120.00 P 65 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 0.011381 0.006571 0.000000 0.00000 SCALE2 0.000000 0.013142 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006824 0.00000