HEADER HYDROLASE 20-OCT-15 5ECT TITLE MYCOBACTERIUM TUBERCULOSIS DUTPASE G143STOP MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DUTPASE,DUTP PYROPHOSPHATASE; COMPND 5 EC: 3.6.1.23; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: DUT, RV2697C, MTCY05A6.18C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HYDROLASE, JELLY-ROLL, TRIMER EXPDTA X-RAY DIFFRACTION AUTHOR G.N.NAGY,I.LEVELES,V.HARMAT,G.B.VERTESSY REVDAT 3 10-JAN-24 5ECT 1 LINK REVDAT 2 21-DEC-16 5ECT 1 JRNL REVDAT 1 02-NOV-16 5ECT 0 JRNL AUTH G.N.NAGY,R.SUARDIAZ,A.LOPATA,O.OZOHANICS,K.VEKEY,B.R.BROOKS, JRNL AUTH 2 I.LEVELES,J.TOTH,B.G.VERTESSY,E.ROSTA JRNL TITL STRUCTURAL CHARACTERIZATION OF ARGININE FINGERS: JRNL TITL 2 IDENTIFICATION OF AN ARGININE FINGER FOR THE PYROPHOSPHATASE JRNL TITL 3 DUTPASES. JRNL REF J. AM. CHEM. SOC. V. 138 15035 2016 JRNL REFN ESSN 1520-5126 JRNL PMID 27740761 JRNL DOI 10.1021/JACS.6B09012 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 33008 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) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.123 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1813 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2459 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 112 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1050 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 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): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.007 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.986 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1126 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1115 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1541 ; 1.899 ; 2.026 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2548 ; 1.249 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 150 ; 6.720 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 39 ;32.469 ;21.282 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 167 ;10.289 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;18.487 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 187 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1250 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 235 ; 0.005 ; 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): 589 ; 5.658 ; 2.132 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 587 ; 5.712 ; 2.133 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 733 ; 7.339 ; 3.180 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 734 ; 7.404 ; 3.189 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 535 ; 4.511 ; 2.200 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 535 ; 4.495 ; 2.200 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 804 ; 5.170 ; 3.228 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1174 ; 7.140 ;17.251 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1175 ; 7.146 ;17.281 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2236 ; 5.038 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 52 ;27.470 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2296 ;16.086 ; 5.000 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 : BABINET MODEL WITH 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 5ECT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000206672. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8729 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34842 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 26.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.950 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: 3HZA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 0.1M TRIS/HCL, REMARK 280 12% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, 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 42.03950 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 42.03950 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 42.03950 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: 14700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 -27.39000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 47.44087 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -54.78000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 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 C TRS A 202 LIES ON A SPECIAL POSITION. REMARK 375 N TRS A 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 311 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 349 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 402 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 408 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 415 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 419 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 425 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 SER A -9 REMARK 465 GLY A 134 REMARK 465 LEU A 135 REMARK 465 ALA A 136 REMARK 465 SER A 137 REMARK 465 ASP A 142 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 -8 OG REMARK 470 ARG A -3 CB CG CD NE CZ NH1 NH2 REMARK 470 SER A -1 OG REMARK 470 MET A 1 CG SD CE REMARK 470 ARG A 46 CZ NH1 NH2 REMARK 470 ASP A 131 CG OD1 OD2 REMARK 470 GLU A 132 CG CD OE1 OE2 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 C TRS A 202 C1 TRS A 202 2565 1.62 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 -25.86 -141.37 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 A 423 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 424 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 425 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH A 426 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH A 427 DISTANCE = 9.89 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 TRS A 202 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 A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUP A 201 O2A REMARK 620 2 DUP A 201 O2B 87.4 REMARK 620 3 DUP A 201 O1G 94.6 87.7 REMARK 620 4 HOH A 305 O 172.9 89.2 91.5 REMARK 620 5 HOH A 372 O 89.3 93.4 176.0 84.7 REMARK 620 6 HOH A 378 O 88.5 175.9 93.3 94.8 85.9 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 DUP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GCY RELATED DB: PDB REMARK 900 4GCY CONTAINS THE H21W VARIANT OF THE SAME PROTEIN. REMARK 900 RELATED ID: 3LOJ RELATED DB: PDB REMARK 900 3LOJ CONTAINS THE H145A VARIANT OF THE SAME PROTEIN. REMARK 900 RELATED ID: 3I93 RELATED DB: PDB REMARK 900 3I93 CONTAINS THE T138STOP VARIANT OF THE SAME PROTEIN. REMARK 900 RELATED ID: 3HZA RELATED DB: PDB REMARK 900 3HZA CONTAINS THE H145W VARIANT OF THE SAME PROTEIN. REMARK 900 RELATED ID: 3H6D RELATED DB: PDB REMARK 900 3H6D CONTAINS THE D28N VARIANT OF THE SAME PROTEIN. REMARK 900 RELATED ID: 2PY4 RELATED DB: PDB REMARK 900 2PY4 CONTAINS THE WILD TYPE FORM OF THE SAME PROTEIN COMPLEXED WITH REMARK 900 MG2+ AND DUPNPP REMARK 900 RELATED ID: 1SJN RELATED DB: PDB REMARK 900 1SJN CONTAINS THE WILD TYPE FORM OF THE SAME PROTEIN COMPLEXED WITH REMARK 900 MG2+ AND DUPNPP REMARK 900 RELATED ID: 1SIX RELATED DB: PDB REMARK 900 1SIX CONTAINS THE WILD TYPE FORM OF THE SAME PROTEIN COMPLEXED WITH REMARK 900 MG2+ AND DUPNPP REMARK 900 RELATED ID: 1MQ7 RELATED DB: PDB REMARK 900 1MQ7 CONTAINS THE WILD TYPE FORM OF THE SAME PROTEIN REMARK 900 RELATED ID: 1SNF RELATED DB: PDB REMARK 900 1SNF CONTAINS THE WILD TYPE FORM OF THE SAME PROTEIN COMPLEXED WITH REMARK 900 MG2+ AND DUPMP REMARK 900 RELATED ID: 1SLH RELATED DB: PDB REMARK 900 1SLH CONTAINS THE WILD TYPE FORM OF THE SAME PROTEIN COMPLEXED WITH REMARK 900 MG2+ AND DUPDP REMARK 900 RELATED ID: 1SMC RELATED DB: PDB REMARK 900 1SMC CONTAINS THE WILD TYPE FORM OF THE SAME PROTEIN COMPLEXED WITH REMARK 900 DUPNPP IN ABSENCE OF MG2+ DBREF 5ECT A 1 142 UNP P9WNS5 DUT_MYCTU 1 142 SEQADV 5ECT MET A -19 UNP P9WNS5 INITIATING METHIONINE SEQADV 5ECT GLY A -18 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT SER A -17 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT SER A -16 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT HIS A -15 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT HIS A -14 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT HIS A -13 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT HIS A -12 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT HIS A -11 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT HIS A -10 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT SER A -9 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT SER A -8 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT GLY A -7 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT LEU A -6 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT VAL A -5 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT PRO A -4 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT ARG A -3 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT GLY A -2 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT SER A -1 UNP P9WNS5 EXPRESSION TAG SEQADV 5ECT HIS A 0 UNP P9WNS5 EXPRESSION TAG SEQRES 1 A 162 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 162 LEU VAL PRO ARG GLY SER HIS MET SER THR THR LEU ALA SEQRES 3 A 162 ILE VAL ARG LEU ASP PRO GLY LEU PRO LEU PRO SER ARG SEQRES 4 A 162 ALA HIS ASP GLY ASP ALA GLY VAL ASP LEU TYR SER ALA SEQRES 5 A 162 GLU ASP VAL GLU LEU ALA PRO GLY ARG ARG ALA LEU VAL SEQRES 6 A 162 ARG THR GLY VAL ALA VAL ALA VAL PRO PHE GLY MET VAL SEQRES 7 A 162 GLY LEU VAL HIS PRO ARG SER GLY LEU ALA THR ARG VAL SEQRES 8 A 162 GLY LEU SER ILE VAL ASN SER PRO GLY THR ILE ASP ALA SEQRES 9 A 162 GLY TYR ARG GLY GLU ILE LYS VAL ALA LEU ILE ASN LEU SEQRES 10 A 162 ASP PRO ALA ALA PRO ILE VAL VAL HIS ARG GLY ASP ARG SEQRES 11 A 162 ILE ALA GLN LEU LEU VAL GLN ARG VAL GLU LEU VAL GLU SEQRES 12 A 162 LEU VAL GLU VAL SER SER PHE ASP GLU ALA GLY LEU ALA SEQRES 13 A 162 SER THR SER ARG GLY ASP HET DUP A 201 28 HET TRS A 202 4 HET MG A 203 1 HET GOL A 204 6 HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DUP C9 H16 N3 O13 P3 FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 MG MG 2+ FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *127(H2 O) HELIX 1 AA1 PRO A -4 HIS A 0 5 5 HELIX 2 AA2 ARG A 64 GLY A 72 1 9 SHEET 1 AA1 2 ALA A 6 ARG A 9 0 SHEET 2 AA1 2 VAL A 49 ALA A 52 -1 O ALA A 50 N VAL A 8 SHEET 1 AA2 4 VAL A 27 TYR A 30 0 SHEET 2 AA2 4 ARG A 110 ARG A 118 -1 O LEU A 114 N VAL A 27 SHEET 3 AA2 4 MET A 57 HIS A 62 -1 N HIS A 62 O GLN A 113 SHEET 4 AA2 4 GLY A 80 ILE A 82 -1 O ILE A 82 N GLY A 59 SHEET 1 AA3 2 VAL A 35 LEU A 37 0 SHEET 2 AA3 2 ILE A 103 VAL A 105 -1 O VAL A 105 N VAL A 35 SHEET 1 AA4 3 ARG A 42 ARG A 46 0 SHEET 2 AA4 3 LYS A 91 ASN A 96 -1 O VAL A 92 N VAL A 45 SHEET 3 AA4 3 LEU A 73 ILE A 75 -1 N SER A 74 O ILE A 95 LINK O2A DUP A 201 MG MG A 203 1555 1555 2.06 LINK O2B DUP A 201 MG MG A 203 1555 1555 2.10 LINK O1G DUP A 201 MG MG A 203 1555 1555 2.03 LINK MG MG A 203 O HOH A 305 1555 3455 2.06 LINK MG MG A 203 O HOH A 372 1555 1555 2.09 LINK MG MG A 203 O HOH A 378 1555 1555 2.15 CISPEP 1 SER A 78 PRO A 79 0 -7.23 SITE 1 AC1 26 ARG A 64 SER A 65 GLY A 66 ASN A 77 SITE 2 AC1 26 GLY A 80 THR A 81 ILE A 82 ASP A 83 SITE 3 AC1 26 TYR A 86 ILE A 90 LYS A 91 GLN A 113 SITE 4 AC1 26 ARG A 140 MG A 203 HOH A 304 HOH A 305 SITE 5 AC1 26 HOH A 322 HOH A 324 HOH A 329 HOH A 334 SITE 6 AC1 26 HOH A 362 HOH A 364 HOH A 372 HOH A 378 SITE 7 AC1 26 HOH A 381 HOH A 414 SITE 1 AC2 4 SER A 74 ILE A 75 VAL A 76 HOH A 344 SITE 1 AC3 4 DUP A 201 HOH A 305 HOH A 372 HOH A 378 SITE 1 AC4 5 ARG A 64 ASP A 109 ARG A 110 HOH A 302 SITE 2 AC4 5 HOH A 380 CRYST1 54.780 54.780 84.079 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 0.018255 0.010539 0.000000 0.00000 SCALE2 0.000000 0.021079 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011894 0.00000