HEADER HYDROLASE 10-JUL-09 3I93 TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DUTPASE STOP138T TITLE 2 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: STOPT138 TRUNCATED DUTPASE: UNP RESIDUES 1-138; COMPND 5 SYNONYM: DUTPASE, DUTP PYROPHOSPHATASE; COMPND 6 EC: 3.6.1.23; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: DUT, MT2771, MTCY05A6.18C, RV2697C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS JELLY-ROLL, ENZYME-LIGAND COMPLEX, HYDROLASE, MAGNESIUM, METAL- KEYWDS 2 BINDING, NUCLEOTIDE METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR I.LEVELES,V.HARMAT,A.LOPATA,J.TOTH,B.G.VERTESSY REVDAT 5 06-SEP-23 3I93 1 REMARK SEQADV LINK REVDAT 4 01-NOV-17 3I93 1 REMARK REVDAT 3 13-JUL-11 3I93 1 VERSN REVDAT 2 01-SEP-10 3I93 1 JRNL REVDAT 1 24-NOV-09 3I93 0 JRNL AUTH E.TAKACS,G.NAGY,I.LEVELES,V.HARMAT,A.LOPATA,J.TOTH, JRNL AUTH 2 B.G.VERTESSY JRNL TITL DIRECT CONTACTS BETWEEN CONSERVED MOTIFS OF DIFFERENT JRNL TITL 2 SUBUNITS PROVIDE MAJOR CONTRIBUTION TO ACTIVE SITE JRNL TITL 3 ORGANIZATION IN HUMAN AND MYCOBACTERIAL DUTPASES. JRNL REF FEBS LETT. V. 584 3047 2010 JRNL REFN ISSN 0014-5793 JRNL PMID 20493855 JRNL DOI 10.1016/J.FEBSLET.2010.05.018 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 11999 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 638 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 875 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1006 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 28.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.11000 REMARK 3 B12 (A**2) : 0.04000 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): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.177 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1077 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1046 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1474 ; 1.549 ; 2.032 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2409 ; 0.616 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 142 ; 6.754 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 35 ;30.010 ;22.857 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 161 ;12.003 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;21.334 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 180 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1182 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 194 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 709 ; 1.017 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 293 ; 0.324 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1140 ; 1.693 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 368 ; 2.705 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 334 ; 4.179 ; 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 -9 A -3 REMARK 3 ORIGIN FOR THE GROUP (A): 15.2822 33.9899 15.2020 REMARK 3 T TENSOR REMARK 3 T11: 0.0716 T22: 0.1230 REMARK 3 T33: 0.1729 T12: -0.0145 REMARK 3 T13: -0.0099 T23: -0.0855 REMARK 3 L TENSOR REMARK 3 L11: 7.5871 L22: 5.3875 REMARK 3 L33: 7.9541 L12: 1.6064 REMARK 3 L13: -1.4685 L23: -6.5245 REMARK 3 S TENSOR REMARK 3 S11: 0.0289 S12: -0.3164 S13: 0.4615 REMARK 3 S21: -0.0631 S22: -0.0817 S23: -0.0605 REMARK 3 S31: 0.0782 S32: 0.1138 S33: 0.0528 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 2 A 134 REMARK 3 ORIGIN FOR THE GROUP (A): 17.5137 19.0328 39.5260 REMARK 3 T TENSOR REMARK 3 T11: 0.0152 T22: 0.0021 REMARK 3 T33: 0.0076 T12: 0.0049 REMARK 3 T13: -0.0053 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.9031 L22: 0.8921 REMARK 3 L33: 0.7349 L12: -0.3587 REMARK 3 L13: 0.1084 L23: -0.0092 REMARK 3 S TENSOR REMARK 3 S11: -0.0011 S12: 0.0164 S13: 0.0483 REMARK 3 S21: -0.0678 S22: -0.0200 S23: 0.0254 REMARK 3 S31: -0.0834 S32: -0.0312 S33: 0.0211 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 200 A 201 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0736 9.5064 39.2435 REMARK 3 T TENSOR REMARK 3 T11: 0.0847 T22: 0.0597 REMARK 3 T33: 0.1231 T12: -0.0152 REMARK 3 T13: 0.0008 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 2.7794 L22: 0.0678 REMARK 3 L33: 3.3890 L12: -0.1926 REMARK 3 L13: -1.3999 L23: -0.2851 REMARK 3 S TENSOR REMARK 3 S11: 0.0167 S12: 0.0805 S13: -0.2310 REMARK 3 S21: -0.0680 S22: -0.0072 S23: 0.0311 REMARK 3 S31: 0.4450 S32: -0.1398 S33: -0.0094 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3I93 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X12 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97861 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI[111] REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13306 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.520 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.15 REMARK 200 R MERGE FOR SHELL (I) : 0.50300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3HZA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M AMMONIUM SULFATE, 50 MM TRIS REMARK 280 -HCL, 12 % GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 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 41.52550 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 41.52550 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 41.52550 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 54.59100 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 27.29550 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 47.27719 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 A 321 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 388 LIES ON A SPECIAL POSITION. 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LEU A 135 REMARK 465 ALA A 136 REMARK 465 SER A 137 REMARK 465 THR A 138 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 SER A -9 OG REMARK 470 ARG A -3 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 22 CG OD1 OD2 REMARK 470 ARG A 46 CZ NH1 NH2 REMARK 470 ARG A 70 NE CZ NH1 NH2 REMARK 470 ARG A 118 CZ NH1 NH2 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 C1 TRS A 203 N TRS A 203 2665 1.84 REMARK 500 N TRS A 203 O1 TRS A 203 3565 1.88 REMARK 500 C1 TRS A 203 C1 TRS A 203 2665 1.89 REMARK 500 C TRS A 202 O1 TRS A 202 3665 1.93 REMARK 500 C TRS A 203 O1 TRS A 203 2665 1.96 REMARK 500 C1 TRS A 202 N TRS A 202 3665 2.15 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 100 -25.71 -145.36 REMARK 500 ALA A 133 11.94 -63.49 REMARK 500 REMARK 500 REMARK: NULL 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 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PY4 RELATED DB: PDB REMARK 900 FULL LENGTH STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS DUTPASE REMARK 900 COMPLEXED WITH MAGNESIUM AND ALPHA,BETA-IMIDO-DUTP REMARK 900 RELATED ID: 3H6D RELATED DB: PDB REMARK 900 STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS DUTPASE D28N MUTANT REMARK 900 RELATED ID: 3HZA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DUTPASE H145W MUTANT DBREF 3I93 A 1 138 UNP P0A552 DUT_MYCTU 1 138 SEQADV 3I93 MET A -19 UNP P0A552 EXPRESSION TAG SEQADV 3I93 GLY A -18 UNP P0A552 EXPRESSION TAG SEQADV 3I93 SER A -17 UNP P0A552 EXPRESSION TAG SEQADV 3I93 SER A -16 UNP P0A552 EXPRESSION TAG SEQADV 3I93 HIS A -15 UNP P0A552 EXPRESSION TAG SEQADV 3I93 HIS A -14 UNP P0A552 EXPRESSION TAG SEQADV 3I93 HIS A -13 UNP P0A552 EXPRESSION TAG SEQADV 3I93 HIS A -12 UNP P0A552 EXPRESSION TAG SEQADV 3I93 HIS A -11 UNP P0A552 EXPRESSION TAG SEQADV 3I93 HIS A -10 UNP P0A552 EXPRESSION TAG SEQADV 3I93 SER A -9 UNP P0A552 EXPRESSION TAG SEQADV 3I93 SER A -8 UNP P0A552 EXPRESSION TAG SEQADV 3I93 GLY A -7 UNP P0A552 EXPRESSION TAG SEQADV 3I93 LEU A -6 UNP P0A552 EXPRESSION TAG SEQADV 3I93 VAL A -5 UNP P0A552 EXPRESSION TAG SEQADV 3I93 PRO A -4 UNP P0A552 EXPRESSION TAG SEQADV 3I93 ARG A -3 UNP P0A552 EXPRESSION TAG SEQADV 3I93 GLY A -2 UNP P0A552 EXPRESSION TAG SEQADV 3I93 SER A -1 UNP P0A552 EXPRESSION TAG SEQADV 3I93 HIS A 0 UNP P0A552 EXPRESSION TAG SEQRES 1 A 158 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 158 LEU VAL PRO ARG GLY SER HIS MET SER THR THR LEU ALA SEQRES 3 A 158 ILE VAL ARG LEU ASP PRO GLY LEU PRO LEU PRO SER ARG SEQRES 4 A 158 ALA HIS ASP GLY ASP ALA GLY VAL ASP LEU TYR SER ALA SEQRES 5 A 158 GLU ASP VAL GLU LEU ALA PRO GLY ARG ARG ALA LEU VAL SEQRES 6 A 158 ARG THR GLY VAL ALA VAL ALA VAL PRO PHE GLY MET VAL SEQRES 7 A 158 GLY LEU VAL HIS PRO ARG SER GLY LEU ALA THR ARG VAL SEQRES 8 A 158 GLY LEU SER ILE VAL ASN SER PRO GLY THR ILE ASP ALA SEQRES 9 A 158 GLY TYR ARG GLY GLU ILE LYS VAL ALA LEU ILE ASN LEU SEQRES 10 A 158 ASP PRO ALA ALA PRO ILE VAL VAL HIS ARG GLY ASP ARG SEQRES 11 A 158 ILE ALA GLN LEU LEU VAL GLN ARG VAL GLU LEU VAL GLU SEQRES 12 A 158 LEU VAL GLU VAL SER SER PHE ASP GLU ALA GLY LEU ALA SEQRES 13 A 158 SER THR HET MG A 200 1 HET DUP A 201 28 HET TRS A 202 4 HET TRS A 203 4 HETNAM MG MAGNESIUM ION HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 MG MG 2+ FORMUL 3 DUP C9 H16 N3 O13 P3 FORMUL 4 TRS 2(C4 H12 N O3 1+) FORMUL 6 HOH *105(H2 O) HELIX 1 1 ARG A 64 GLY A 72 1 9 SHEET 1 A 4 ALA A 6 ARG A 9 0 SHEET 2 A 4 ARG A 42 ALA A 52 -1 O ALA A 50 N VAL A 8 SHEET 3 A 4 GLU A 89 ASN A 96 -1 O VAL A 92 N VAL A 45 SHEET 4 A 4 LEU A 73 ILE A 75 -1 N SER A 74 O ILE A 95 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 LINK C TRS A 202 C1 TRS A 202 1555 3665 1.42 LINK C TRS A 203 C1 TRS A 203 1555 2665 1.08 CISPEP 1 SER A 2 THR A 3 0 27.81 CISPEP 2 SER A 78 PRO A 79 0 -0.23 SITE 1 AC1 4 DUP A 201 HOH A 383 HOH A 384 HOH A 395 SITE 1 AC2 21 ARG A 64 SER A 65 GLY A 66 ASN A 77 SITE 2 AC2 21 GLY A 80 THR A 81 ILE A 82 ASP A 83 SITE 3 AC2 21 TYR A 86 GLU A 89 ILE A 90 LYS A 91 SITE 4 AC2 21 GLN A 113 MG A 200 HOH A 323 HOH A 324 SITE 5 AC2 21 HOH A 353 HOH A 355 HOH A 383 HOH A 384 SITE 6 AC2 21 HOH A 395 SITE 1 AC3 4 SER A 74 ILE A 75 VAL A 76 HOH A 309 SITE 1 AC4 4 ARG A 9 PRO A 12 HOH A 356 HOH A 389 CRYST1 54.591 54.591 83.051 90.00 90.00 120.00 P 63 6 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 0.018318 0.010576 0.000000 0.00000 SCALE2 0.000000 0.021152 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012041 0.00000