HEADER HYDROLASE 05-MAR-04 1SLH TITLE MYCOBACTERIUM TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND DUDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: DUTPASE, DUTP PYROPHOSPHATASE; COMPND 5 EC: 3.6.1.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: DUT, RV2697C, MT2771, MTCY05A6.18C, MB2716C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21PRO; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET28B KEYWDS JELLY-ROLL, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 TB STRUCTURAL GENOMICS CONSORTIUM, TBSGC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SAWAYA,S.CHAN,B.SEGELKE,T.LEKIN,H.KRUPKA,U.S.CHO,M.-Y.KIM,M.SO, AUTHOR 2 C.-Y.KIM,C.M.NARANJO,Y.C.ROGERS,M.S.PARK,G.S.WALDO,I.PASHKOV, AUTHOR 3 D.CASCIO,T.O.YEATES,J.L.PERRY,T.C.TERWILLIGER,D.EISENBERG,TB AUTHOR 4 STRUCTURAL GENOMICS CONSORTIUM (TBSGC) REVDAT 4 23-AUG-23 1SLH 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1SLH 1 VERSN REVDAT 2 11-JAN-05 1SLH 1 JRNL AUTHOR KEYWDS REMARK REVDAT 1 16-MAR-04 1SLH 0 JRNL AUTH S.CHAN,B.SEGELKE,T.LEKIN,H.KRUPKA,U.S.CHO,M.-Y.KIM,M.SO, JRNL AUTH 2 C.-Y.KIM,C.M.NARANJO,Y.C.ROGERS,M.S.PARK,G.S.WALDO, JRNL AUTH 3 I.PASHKOV,D.CASCIO,J.L.PERRY,M.R.SAWAYA JRNL TITL CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS DUTPASE: JRNL TITL 2 INSIGHTS INTO THE CATALYTIC MECHANISM. JRNL REF J.MOL.BIOL. V. 341 503 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15276840 JRNL DOI 10.1016/J.JMB.2004.06.028 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 93.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1365533.820 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14034 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 677 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2184 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 114 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2975 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.30 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) : 7.20000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.38 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.53 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.350 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 19.05 REMARK 3 REMARK 3 NCS MODEL : CONSTR REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : UDP.PAR REMARK 3 PARAMETER FILE 5 : TRS.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : UDP.TOP REMARK 3 TOPOLOGY FILE 5 : TRS.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SLH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-D REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14054 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13800 REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50700 REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: 1MQ7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MAGNESIUM NITRATE, TRIS, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 33.59733 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 67.19467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.19467 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 33.59733 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HOMO-TRIMER. IT IS CONTAINED REMARK 300 WITHIN THE ASYMMETRIC UNIT. 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 28710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -164.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 67.19467 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 137 REMARK 465 THR A 138 REMARK 465 SER A 139 REMARK 465 ARG A 140 REMARK 465 GLY A 141 REMARK 465 ASP A 142 REMARK 465 GLY A 143 REMARK 465 GLY A 144 REMARK 465 HIS A 145 REMARK 465 GLY A 146 REMARK 465 SER A 147 REMARK 465 SER A 148 REMARK 465 GLY A 149 REMARK 465 GLY A 150 REMARK 465 HIS A 151 REMARK 465 ALA A 152 REMARK 465 SER A 153 REMARK 465 LEU A 154 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 GLY B 143 REMARK 465 GLY B 144 REMARK 465 HIS B 145 REMARK 465 GLY B 146 REMARK 465 SER B 147 REMARK 465 SER B 148 REMARK 465 GLY B 149 REMARK 465 GLY B 150 REMARK 465 HIS B 151 REMARK 465 ALA B 152 REMARK 465 SER B 153 REMARK 465 LEU B 154 REMARK 465 MET C -19 REMARK 465 GLY C -18 REMARK 465 SER C -17 REMARK 465 SER C -16 REMARK 465 HIS C -15 REMARK 465 HIS C -14 REMARK 465 HIS C -13 REMARK 465 HIS C -12 REMARK 465 HIS C -11 REMARK 465 HIS C -10 REMARK 465 SER C -9 REMARK 465 SER C -8 REMARK 465 GLY C -7 REMARK 465 LEU C -6 REMARK 465 VAL C -5 REMARK 465 PRO C -4 REMARK 465 ARG C -3 REMARK 465 GLY C -2 REMARK 465 SER C -1 REMARK 465 HIS C 0 REMARK 465 ASP C 131 REMARK 465 GLU C 132 REMARK 465 ALA C 133 REMARK 465 GLY C 134 REMARK 465 LEU C 135 REMARK 465 ALA C 136 REMARK 465 SER C 137 REMARK 465 THR C 138 REMARK 465 SER C 139 REMARK 465 ARG C 140 REMARK 465 GLY C 141 REMARK 465 ASP C 142 REMARK 465 GLY C 143 REMARK 465 GLY C 144 REMARK 465 HIS C 145 REMARK 465 GLY C 146 REMARK 465 SER C 147 REMARK 465 SER C 148 REMARK 465 GLY C 149 REMARK 465 GLY C 150 REMARK 465 HIS C 151 REMARK 465 ALA C 152 REMARK 465 SER C 153 REMARK 465 LEU C 154 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 87 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP C 28 OD1 - CG - OD2 ANGL. DEV. = -11.6 DEGREES REMARK 500 ASP C 28 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG C 87 NE - CZ - NH1 ANGL. DEV. = -3.1 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 ALA A 52 77.10 -111.88 REMARK 500 ALA A 112 -177.61 -175.83 REMARK 500 ALA B 43 140.53 -172.08 REMARK 500 ALA C 43 135.87 -170.30 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 C2171 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUD A2170 O2B REMARK 620 2 DUD A2170 O1A 70.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A3171 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 542 O REMARK 620 2 HOH B 543 O 106.7 REMARK 620 3 DUD B3170 O1A 79.6 53.6 REMARK 620 4 DUD B3170 O2B 86.4 122.3 75.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1171 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUD C1170 O3A REMARK 620 2 DUD C1170 O1B 48.0 REMARK 620 3 DUD C1170 O1A 47.3 95.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 2171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUD C 1170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUD A 2170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUD B 3170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SM8 RELATED DB: PDB REMARK 900 M. TUBERCULOSIS DUTPASE COMPLEXED WITH CHROMIUM AND DUTP REMARK 900 RELATED ID: 1SMC RELATED DB: PDB REMARK 900 M. TUBERCULOSIS DUTPASE COMPLEXED WITH DUTP IN THE ABSENCE OF METAL REMARK 900 IONS REMARK 900 RELATED ID: 1SJN RELATED DB: PDB REMARK 900 M. TUBERCULOSIS DUTPASE COMPLEXED WITH ALPHA,BETA-IMIDO-DUTP REMARK 900 RELATED ID: 1SIX RELATED DB: PDB REMARK 900 M. TUBERCULOSIS DUTPASE COMPLEXED WITH ALPHA,BETA-IMIDO-DUTP REMARK 900 RELATED ID: 1MQ7 RELATED DB: PDB REMARK 900 M. TUBERCULOSIS DUTPASE UNLIGANDED REMARK 900 RELATED ID: RV2697C RELATED DB: TARGETDB DBREF 1SLH A 1 154 UNP P0A552 DUT_MYCTU 1 154 DBREF 1SLH B 1 154 UNP P0A552 DUT_MYCTU 1 154 DBREF 1SLH C 1 154 UNP P0A552 DUT_MYCTU 1 154 SEQADV 1SLH MET A -19 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH GLY A -18 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER A -17 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER A -16 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH HIS A -15 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS A -14 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS A -13 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS A -12 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS A -11 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS A -10 UNP P0A552 EXPRESSION TAG SEQADV 1SLH SER A -9 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER A -8 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH GLY A -7 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH LEU A -6 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH VAL A -5 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH PRO A -4 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH ARG A -3 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH GLY A -2 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER A -1 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH HIS A 0 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH MET B -19 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH GLY B -18 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER B -17 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER B -16 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH HIS B -15 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS B -14 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS B -13 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS B -12 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS B -11 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS B -10 UNP P0A552 EXPRESSION TAG SEQADV 1SLH SER B -9 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER B -8 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH GLY B -7 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH LEU B -6 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH VAL B -5 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH PRO B -4 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH ARG B -3 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH GLY B -2 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER B -1 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH HIS B 0 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH MET C -19 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH GLY C -18 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER C -17 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER C -16 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH HIS C -15 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS C -14 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS C -13 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS C -12 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS C -11 UNP P0A552 EXPRESSION TAG SEQADV 1SLH HIS C -10 UNP P0A552 EXPRESSION TAG SEQADV 1SLH SER C -9 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER C -8 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH GLY C -7 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH LEU C -6 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH VAL C -5 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH PRO C -4 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH ARG C -3 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH GLY C -2 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH SER C -1 UNP P0A552 CLONING ARTIFACT SEQADV 1SLH HIS C 0 UNP P0A552 CLONING ARTIFACT SEQRES 1 A 174 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 174 LEU VAL PRO ARG GLY SER HIS MET SER THR THR LEU ALA SEQRES 3 A 174 ILE VAL ARG LEU ASP PRO GLY LEU PRO LEU PRO SER ARG SEQRES 4 A 174 ALA HIS ASP GLY ASP ALA GLY VAL ASP LEU TYR SER ALA SEQRES 5 A 174 GLU ASP VAL GLU LEU ALA PRO GLY ARG ARG ALA LEU VAL SEQRES 6 A 174 ARG THR GLY VAL ALA VAL ALA VAL PRO PHE GLY MET VAL SEQRES 7 A 174 GLY LEU VAL HIS PRO ARG SER GLY LEU ALA THR ARG VAL SEQRES 8 A 174 GLY LEU SER ILE VAL ASN SER PRO GLY THR ILE ASP ALA SEQRES 9 A 174 GLY TYR ARG GLY GLU ILE LYS VAL ALA LEU ILE ASN LEU SEQRES 10 A 174 ASP PRO ALA ALA PRO ILE VAL VAL HIS ARG GLY ASP ARG SEQRES 11 A 174 ILE ALA GLN LEU LEU VAL GLN ARG VAL GLU LEU VAL GLU SEQRES 12 A 174 LEU VAL GLU VAL SER SER PHE ASP GLU ALA GLY LEU ALA SEQRES 13 A 174 SER THR SER ARG GLY ASP GLY GLY HIS GLY SER SER GLY SEQRES 14 A 174 GLY HIS ALA SER LEU SEQRES 1 B 174 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 174 LEU VAL PRO ARG GLY SER HIS MET SER THR THR LEU ALA SEQRES 3 B 174 ILE VAL ARG LEU ASP PRO GLY LEU PRO LEU PRO SER ARG SEQRES 4 B 174 ALA HIS ASP GLY ASP ALA GLY VAL ASP LEU TYR SER ALA SEQRES 5 B 174 GLU ASP VAL GLU LEU ALA PRO GLY ARG ARG ALA LEU VAL SEQRES 6 B 174 ARG THR GLY VAL ALA VAL ALA VAL PRO PHE GLY MET VAL SEQRES 7 B 174 GLY LEU VAL HIS PRO ARG SER GLY LEU ALA THR ARG VAL SEQRES 8 B 174 GLY LEU SER ILE VAL ASN SER PRO GLY THR ILE ASP ALA SEQRES 9 B 174 GLY TYR ARG GLY GLU ILE LYS VAL ALA LEU ILE ASN LEU SEQRES 10 B 174 ASP PRO ALA ALA PRO ILE VAL VAL HIS ARG GLY ASP ARG SEQRES 11 B 174 ILE ALA GLN LEU LEU VAL GLN ARG VAL GLU LEU VAL GLU SEQRES 12 B 174 LEU VAL GLU VAL SER SER PHE ASP GLU ALA GLY LEU ALA SEQRES 13 B 174 SER THR SER ARG GLY ASP GLY GLY HIS GLY SER SER GLY SEQRES 14 B 174 GLY HIS ALA SER LEU SEQRES 1 C 174 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 C 174 LEU VAL PRO ARG GLY SER HIS MET SER THR THR LEU ALA SEQRES 3 C 174 ILE VAL ARG LEU ASP PRO GLY LEU PRO LEU PRO SER ARG SEQRES 4 C 174 ALA HIS ASP GLY ASP ALA GLY VAL ASP LEU TYR SER ALA SEQRES 5 C 174 GLU ASP VAL GLU LEU ALA PRO GLY ARG ARG ALA LEU VAL SEQRES 6 C 174 ARG THR GLY VAL ALA VAL ALA VAL PRO PHE GLY MET VAL SEQRES 7 C 174 GLY LEU VAL HIS PRO ARG SER GLY LEU ALA THR ARG VAL SEQRES 8 C 174 GLY LEU SER ILE VAL ASN SER PRO GLY THR ILE ASP ALA SEQRES 9 C 174 GLY TYR ARG GLY GLU ILE LYS VAL ALA LEU ILE ASN LEU SEQRES 10 C 174 ASP PRO ALA ALA PRO ILE VAL VAL HIS ARG GLY ASP ARG SEQRES 11 C 174 ILE ALA GLN LEU LEU VAL GLN ARG VAL GLU LEU VAL GLU SEQRES 12 C 174 LEU VAL GLU VAL SER SER PHE ASP GLU ALA GLY LEU ALA SEQRES 13 C 174 SER THR SER ARG GLY ASP GLY GLY HIS GLY SER SER GLY SEQRES 14 C 174 GLY HIS ALA SER LEU HET MG A3171 1 HET DUD A2170 24 HET TRS A 504 8 HET TRS A 505 8 HET MG B1171 1 HET DUD B3170 24 HET MG C2171 1 HET DUD C1170 24 HETNAM MG MAGNESIUM ION HETNAM DUD DEOXYURIDINE-5'-DIPHOSPHATE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 4 MG 3(MG 2+) FORMUL 5 DUD 3(C9 H14 N2 O11 P2) FORMUL 6 TRS 2(C4 H12 N O3 1+) FORMUL 12 HOH *40(H2 O) HELIX 1 1 ARG A 64 VAL A 71 1 8 HELIX 2 2 SER A 129 GLY A 134 1 6 HELIX 3 3 ARG B 64 VAL B 71 1 8 HELIX 4 4 ARG C 64 GLY C 72 1 9 SHEET 1 A 3 VAL A 49 ALA A 52 0 SHEET 2 A 3 THR A 4 ARG A 9 -1 N VAL A 8 O ALA A 50 SHEET 3 A 3 GLU B 123 GLU B 126 1 O VAL B 125 N LEU A 5 SHEET 1 B 4 VAL A 27 TYR A 30 0 SHEET 2 B 4 ARG A 110 ARG A 118 -1 O LEU A 114 N VAL A 27 SHEET 3 B 4 MET A 57 HIS A 62 -1 N HIS A 62 O GLN A 113 SHEET 4 B 4 GLY A 80 ASP A 83 -1 O ILE A 82 N GLY A 59 SHEET 1 C 2 VAL A 35 LEU A 37 0 SHEET 2 C 2 ILE A 103 VAL A 105 -1 O VAL A 105 N VAL A 35 SHEET 1 D 3 ARG A 42 ARG A 46 0 SHEET 2 D 3 LYS A 91 ASN A 96 -1 O VAL A 92 N VAL A 45 SHEET 3 D 3 LEU A 73 ILE A 75 -1 N SER A 74 O ILE A 95 SHEET 1 E 3 GLU A 123 VAL A 127 0 SHEET 2 E 3 THR C 4 ARG C 9 1 O LEU C 5 N GLU A 123 SHEET 3 E 3 VAL C 49 ALA C 52 -1 O ALA C 50 N VAL C 8 SHEET 1 F 3 VAL B 49 ALA B 52 0 SHEET 2 F 3 THR B 4 ARG B 9 -1 N VAL B 8 O ALA B 50 SHEET 3 F 3 GLU C 123 GLU C 126 1 O GLU C 123 N LEU B 5 SHEET 1 G 4 VAL B 27 TYR B 30 0 SHEET 2 G 4 ARG B 110 ARG B 118 -1 O LEU B 114 N VAL B 27 SHEET 3 G 4 MET B 57 PRO B 63 -1 N LEU B 60 O LEU B 115 SHEET 4 G 4 GLY B 80 ASP B 83 -1 O ILE B 82 N GLY B 59 SHEET 1 H 2 VAL B 35 LEU B 37 0 SHEET 2 H 2 ILE B 103 VAL B 105 -1 O ILE B 103 N LEU B 37 SHEET 1 I 3 ARG B 42 ARG B 46 0 SHEET 2 I 3 LYS B 91 ASN B 96 -1 O VAL B 92 N VAL B 45 SHEET 3 I 3 LEU B 73 ILE B 75 -1 N SER B 74 O ILE B 95 SHEET 1 J 4 VAL C 27 TYR C 30 0 SHEET 2 J 4 ARG C 110 ARG C 118 -1 O LEU C 114 N VAL C 27 SHEET 3 J 4 MET C 57 HIS C 62 -1 N VAL C 58 O GLN C 117 SHEET 4 J 4 GLY C 80 ILE C 82 -1 O ILE C 82 N GLY C 59 SHEET 1 K 2 VAL C 35 LEU C 37 0 SHEET 2 K 2 ILE C 103 VAL C 105 -1 O VAL C 105 N VAL C 35 SHEET 1 L 3 ARG C 42 ARG C 46 0 SHEET 2 L 3 LYS C 91 ASN C 96 -1 O VAL C 92 N VAL C 45 SHEET 3 L 3 LEU C 73 ILE C 75 -1 N SER C 74 O ILE C 95 LINK O2B DUD A2170 MG MG C2171 1555 1555 2.43 LINK O1A DUD A2170 MG MG C2171 1555 1555 2.39 LINK MG MG A3171 O HOH B 542 1555 1555 1.73 LINK MG MG A3171 O HOH B 543 1555 1555 2.84 LINK MG MG A3171 O1A DUD B3170 1555 1555 2.33 LINK MG MG A3171 O2B DUD B3170 1555 1555 2.24 LINK MG MG B1171 O3A DUD C1170 1555 1555 3.07 LINK MG MG B1171 O1B DUD C1170 1555 1555 2.54 LINK MG MG B1171 O1A DUD C1170 1555 1555 3.03 CISPEP 1 SER A 78 PRO A 79 0 -0.20 CISPEP 2 SER B 78 PRO B 79 0 -3.58 CISPEP 3 SER C 78 PRO C 79 0 -0.30 SITE 1 AC1 1 DUD C1170 SITE 1 AC2 2 DUD A2170 ASP C 28 SITE 1 AC3 3 HOH B 542 HOH B 543 DUD B3170 SITE 1 AC4 15 ARG B 64 SER B 65 GLY B 66 GLN B 113 SITE 2 AC4 15 MG B1171 ASN C 77 GLY C 80 THR C 81 SITE 3 AC4 15 ILE C 82 ASP C 83 TYR C 86 GLU C 89 SITE 4 AC4 15 LYS C 91 HOH C 508 HOH C 513 SITE 1 AC5 13 ASN A 77 THR A 81 ASP A 83 TYR A 86 SITE 2 AC5 13 GLU A 89 ILE A 90 LYS A 91 HOH A 506 SITE 3 AC5 13 HOH A 516 ARG C 64 SER C 65 GLY C 66 SITE 4 AC5 13 MG C2171 SITE 1 AC6 16 ARG A 64 SER A 65 GLY A 66 HOH A 514 SITE 2 AC6 16 MG A3171 ASN B 77 GLY B 80 THR B 81 SITE 3 AC6 16 ILE B 82 ASP B 83 TYR B 86 ILE B 90 SITE 4 AC6 16 LYS B 91 HOH B 530 HOH B 542 HOH B 543 SITE 1 AC7 11 LEU A 60 HIS A 62 PRO A 79 GLN A 117 SITE 2 AC7 11 LEU B 60 HIS B 62 PRO B 79 GLN B 117 SITE 3 AC7 11 HIS C 62 PRO C 79 GLN C 117 SITE 1 AC8 10 SER A 74 ILE A 75 VAL A 76 SER B 74 SITE 2 AC8 10 ILE B 75 VAL B 76 LEU B 97 SER C 74 SITE 3 AC8 10 ILE C 75 VAL C 76 CRYST1 108.273 108.273 100.792 90.00 90.00 120.00 P 31 2 1 18 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 0.009236 0.005332 0.000000 0.00000 SCALE2 0.000000 0.010665 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009921 0.00000