HEADER HYDROLASE 21-OCT-15 5EDD TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DUTPASE R140K, H145W TITLE 2 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, MRA_2725; 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 JELLY-ROLL, ENZYME-LIGAND COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.N.NAGY,I.LEVELES,A.LOPATA,V.HARMAT,J.TOTH,G.B.VERTESSY REVDAT 3 10-JAN-24 5EDD 1 LINK REVDAT 2 21-DEC-16 5EDD 1 JRNL REVDAT 1 02-NOV-16 5EDD 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. 1.97 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9690 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 495 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 704 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1026 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.08000 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): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.320 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1079 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1056 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1481 ; 2.005 ; 2.030 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2413 ; 0.938 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 143 ;14.529 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 34 ;33.434 ;22.353 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 153 ;12.356 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;17.977 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 182 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1195 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 213 ; 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): 576 ; 1.433 ; 1.641 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 574 ; 1.412 ; 1.637 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 717 ; 2.218 ; 2.448 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 718 ; 2.217 ; 2.452 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 503 ; 1.814 ; 1.787 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 499 ; 1.819 ; 1.789 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 762 ; 2.757 ; 2.619 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1186 ; 5.586 ;14.582 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1119 ; 5.043 ;13.640 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 -10 A 5 REMARK 3 ORIGIN FOR THE GROUP (A): 33.6230 0.6366 -23.2371 REMARK 3 T TENSOR REMARK 3 T11: 0.0442 T22: 0.0260 REMARK 3 T33: 0.0274 T12: 0.0101 REMARK 3 T13: -0.0074 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 1.1034 L22: 1.4465 REMARK 3 L33: 5.8010 L12: 0.5626 REMARK 3 L13: -2.5293 L23: -1.3195 REMARK 3 S TENSOR REMARK 3 S11: -0.1210 S12: 0.0480 S13: -0.0644 REMARK 3 S21: -0.0046 S22: -0.0289 S23: -0.1642 REMARK 3 S31: 0.2829 S32: -0.1022 S33: 0.1500 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 6 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): 26.8582 -3.4159 0.7693 REMARK 3 T TENSOR REMARK 3 T11: 0.0355 T22: 0.0289 REMARK 3 T33: 0.0374 T12: 0.0050 REMARK 3 T13: -0.0029 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.0760 L22: 0.3934 REMARK 3 L33: 0.1298 L12: -0.0701 REMARK 3 L13: 0.0456 L23: -0.1972 REMARK 3 S TENSOR REMARK 3 S11: 0.0033 S12: -0.0140 S13: 0.0398 REMARK 3 S21: -0.0088 S22: 0.0010 S23: -0.0168 REMARK 3 S31: 0.0005 S32: 0.0023 S33: -0.0043 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 124 A 133 REMARK 3 ORIGIN FOR THE GROUP (A): 11.0378 -33.2451 -13.3004 REMARK 3 T TENSOR REMARK 3 T11: 0.0247 T22: 0.0567 REMARK 3 T33: 0.1343 T12: -0.0093 REMARK 3 T13: -0.0111 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 2.7125 L22: 0.2071 REMARK 3 L33: 4.6123 L12: 0.3839 REMARK 3 L13: 2.0532 L23: -0.3716 REMARK 3 S TENSOR REMARK 3 S11: 0.0329 S12: 0.3663 S13: -0.0583 REMARK 3 S21: -0.0353 S22: 0.0736 S23: 0.0415 REMARK 3 S31: 0.1907 S32: 0.2108 S33: -0.1066 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 5EDD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000206548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54056 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT EOS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10220 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 41.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.510 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3HZA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 0.1M TRIS/HCL, REMARK 280 12% GLYCEROL, 6.7 MM DUPNPP, 20 MM MAGNESIUM CHLORIDE, VAPOR REMARK 280 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 41.91350 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 41.91350 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 41.91350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 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 27.52600 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -47.67643 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 55.05200 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 201 LIES ON A SPECIAL POSITION. REMARK 375 N TRS A 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 339 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 412 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 424 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 442 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 451 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 457 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 458 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 459 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 GLY A 134 REMARK 465 LEU A 135 REMARK 465 ALA A 136 REMARK 465 SER A 137 REMARK 465 THR A 138 REMARK 465 SER A 139 REMARK 465 LYS A 140 REMARK 465 GLY A 141 REMARK 465 ASP A 142 REMARK 465 GLY A 143 REMARK 465 GLY A 144 REMARK 465 TRP 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 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 HIS A -10 CG ND1 CD2 CE1 NE2 REMARK 470 SER A -8 OG REMARK 470 ARG A -3 CG CD NE CZ NH1 NH2 REMARK 470 MET A 1 CG SD CE REMARK 470 SER A 2 OG REMARK 470 ASP A 22 CG OD1 OD2 REMARK 470 ARG A 46 NE CZ NH1 NH2 REMARK 470 ARG A 118 NE 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 IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 370 O HOH A 433 2.02 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 -27.39 -144.22 REMARK 500 ASP A 131 -70.55 -37.96 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 458 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A 459 DISTANCE = 6.63 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUP A 202 O1A REMARK 620 2 DUP A 202 O1B 85.7 REMARK 620 3 DUP A 202 O2G 89.3 86.6 REMARK 620 4 HOH A 313 O 168.6 85.8 82.7 REMARK 620 5 HOH A 322 O 96.2 90.4 173.6 91.4 REMARK 620 6 HOH A 377 O 91.8 174.3 88.2 95.9 95.0 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 TRS A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DUP 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GCY RELATED DB: PDB REMARK 900 4GCY CONTAINS THE SAME PROTEIN WITH ANOTHER MUTATION REMARK 900 RELATED ID: 3LOJ RELATED DB: PDB REMARK 900 3LOJ CONTAINS THE SAME PROTEIN WITH ANOTHER MUTATION REMARK 900 RELATED ID: 3H6D RELATED DB: PDB REMARK 900 3H6D CONTAINS THE SAME PROTEIN WITH ANOTHER MUTATION REMARK 900 RELATED ID: 3HZA RELATED DB: PDB REMARK 900 3HZA CONTAINS THE SAME PROTEIN WITH ANOTHER MUTATION REMARK 900 RELATED ID: 3I93 RELATED DB: PDB REMARK 900 3I93 CONTAINS THE SAME PROTEIN WITH A C TERMINAL TRUNCATION REMARK 900 RELATED ID: 2PY4 RELATED DB: PDB REMARK 900 2PY4 CONTAINS THE WILD-TYPE FORM OF THE SAME PROTEIN DBREF 5EDD A 1 154 UNP A5U649 DUT_MYCTA 1 154 SEQADV 5EDD MET A -19 UNP A5U649 INITIATING METHIONINE SEQADV 5EDD GLY A -18 UNP A5U649 EXPRESSION TAG SEQADV 5EDD SER A -17 UNP A5U649 EXPRESSION TAG SEQADV 5EDD SER A -16 UNP A5U649 EXPRESSION TAG SEQADV 5EDD HIS A -15 UNP A5U649 EXPRESSION TAG SEQADV 5EDD HIS A -14 UNP A5U649 EXPRESSION TAG SEQADV 5EDD HIS A -13 UNP A5U649 EXPRESSION TAG SEQADV 5EDD HIS A -12 UNP A5U649 EXPRESSION TAG SEQADV 5EDD HIS A -11 UNP A5U649 EXPRESSION TAG SEQADV 5EDD HIS A -10 UNP A5U649 EXPRESSION TAG SEQADV 5EDD SER A -9 UNP A5U649 EXPRESSION TAG SEQADV 5EDD SER A -8 UNP A5U649 EXPRESSION TAG SEQADV 5EDD GLY A -7 UNP A5U649 EXPRESSION TAG SEQADV 5EDD LEU A -6 UNP A5U649 EXPRESSION TAG SEQADV 5EDD VAL A -5 UNP A5U649 EXPRESSION TAG SEQADV 5EDD PRO A -4 UNP A5U649 EXPRESSION TAG SEQADV 5EDD ARG A -3 UNP A5U649 EXPRESSION TAG SEQADV 5EDD GLY A -2 UNP A5U649 EXPRESSION TAG SEQADV 5EDD SER A -1 UNP A5U649 EXPRESSION TAG SEQADV 5EDD HIS A 0 UNP A5U649 EXPRESSION TAG SEQADV 5EDD LYS A 140 UNP A5U649 ARG 140 ENGINEERED MUTATION SEQADV 5EDD TRP A 145 UNP A5U649 HIS 145 ENGINEERED MUTATION 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 LYS GLY ASP GLY GLY TRP GLY SER SER GLY SEQRES 14 A 174 GLY HIS ALA SER LEU HET TRS A 201 8 HET DUP A 202 28 HET MG A 203 1 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN TRS TRIS BUFFER FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 DUP C9 H16 N3 O13 P3 FORMUL 4 MG MG 2+ FORMUL 5 HOH *159(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 ILE A 7 ARG A 9 0 SHEET 2 AA1 2 VAL A 49 VAL A 51 -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 LEU A 60 O LEU A 115 SHEET 4 AA2 4 GLY A 80 ASP A 83 -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 O1A DUP A 202 MG MG A 203 1555 1555 2.08 LINK O1B DUP A 202 MG MG A 203 1555 1555 2.21 LINK O2G DUP A 202 MG MG A 203 1555 1555 2.09 LINK MG MG A 203 O HOH A 313 1555 2545 2.24 LINK MG MG A 203 O HOH A 322 1555 2545 1.99 LINK MG MG A 203 O HOH A 377 1555 1555 2.05 CISPEP 1 SER A 78 PRO A 79 0 -3.86 SITE 1 AC1 4 SER A 74 ILE A 75 VAL A 76 HOH A 354 SITE 1 AC2 27 ARG A 64 SER A 65 GLY A 66 ASN A 77 SITE 2 AC2 27 GLY A 80 THR A 81 ILE A 82 ASP A 83 SITE 3 AC2 27 TYR A 86 GLU A 89 ILE A 90 LYS A 91 SITE 4 AC2 27 GLN A 113 MG A 203 HOH A 302 HOH A 304 SITE 5 AC2 27 HOH A 310 HOH A 313 HOH A 316 HOH A 322 SITE 6 AC2 27 HOH A 323 HOH A 326 HOH A 330 HOH A 334 SITE 7 AC2 27 HOH A 348 HOH A 351 HOH A 377 SITE 1 AC3 4 DUP A 202 HOH A 313 HOH A 322 HOH A 377 CRYST1 55.052 55.052 83.827 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 0.018165 0.010487 0.000000 0.00000 SCALE2 0.000000 0.020975 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011929 0.00000