HEADER HYDROLASE 25-OCT-14 4WS5 TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS URACIL-DNA GLYCOSYLASE TITLE 2 IN COMPLEX WITH 5-NITROURACIL, FORM III COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UDG; COMPND 5 EC: 3.2.2.27; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: ATCC 25618 / H37RV; SOURCE 5 GENE: UNG, RV2976C, MTCY349.11; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSETB MTUUDG KEYWDS DNA-REPAIR, EXCISION REPAIR, CONFORMATIONAL SELECTION, LIGAND- KEYWDS 2 BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.M.ARIF,K.GEETHANANDAN,P.MISHRA,A.SUROLIA,U.VARSHNEY,M.VIJAYAN REVDAT 4 27-SEP-23 4WS5 1 REMARK REVDAT 3 22-NOV-17 4WS5 1 SOURCE REMARK REVDAT 2 22-JUL-15 4WS5 1 JRNL REVDAT 1 15-JUL-15 4WS5 0 JRNL AUTH S.M.ARIF,K.GEETHANANDAN,P.MISHRA,A.SUROLIA,U.VARSHNEY, JRNL AUTH 2 M.VIJAYAN JRNL TITL STRUCTURAL PLASTICITY IN MYCOBACTERIUM TUBERCULOSIS JRNL TITL 2 URACIL-DNA GLYCOSYLASE (MTUNG) AND ITS FUNCTIONAL JRNL TITL 3 IMPLICATIONS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 1514 2015 JRNL REFN ESSN 1399-0047 JRNL PMID 26143923 JRNL DOI 10.1107/S1399004715009311 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.S.KAUSHAL,R.K.TALAWAR,U.VARSHNEY,M.VIJAYAN REMARK 1 TITL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM MYCOBACTERIUM REMARK 1 TITL 2 TUBERCULOSIS: INSIGHTS INTO INTERACTIONS WITH LIGANDS. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 66 887 2010 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 20693660 REMARK 1 DOI 10.1107/S1744309110023043 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.S.KAUSHAL,R.K.TALAWAR,P.D.KRISHNA,U.VARSHNEY,M.VIJAYAN REMARK 1 TITL UNIQUE FEATURES OF THE STRUCTURE AND INTERACTIONS OF REMARK 1 TITL 2 MYCOBACTERIAL URACIL-DNA GLYCOSYLASE: STRUCTURE OF A COMPLEX REMARK 1 TITL 3 OF THE MYCOBACTERIUM TUBERCULOSIS ENZYME IN COMPARISON WITH REMARK 1 TITL 4 THOSE FROM OTHER SOURCES. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 64 551 2008 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 18453691 REMARK 1 DOI 10.1107/S090744490800512X REMARK 1 REFERENCE 3 REMARK 1 AUTH K.SAIKRISHNAN,M.BIDYA SAGAR,R.RAVISHANKAR,S.ROY, REMARK 1 AUTH 2 K.PURNAPATRE,P.HANDA,U.VARSHNEY,M.VIJAYAN REMARK 1 TITL DOMAIN CLOSURE AND ACTION OF URACIL DNA GLYCOSYLASE (UDG): REMARK 1 TITL 2 STRUCTURES OF NEW CRYSTAL FORMS CONTAINING THE ESCHERICHIA REMARK 1 TITL 3 COLI ENZYME AND A COMPARATIVE STUDY OF THE KNOWN STRUCTURES REMARK 1 TITL 4 INVOLVING UDG. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 1269 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 12136137 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.RAVISHANKAR,M.BIDYA SAGAR,S.ROY,K.PURNAPATRE,P.HANDA, REMARK 1 AUTH 2 U.VARSHNEY,M.VIJAYAN REMARK 1 TITL X-RAY ANALYSIS OF A COMPLEX OF ESCHERICHIA COLI URACIL DNA REMARK 1 TITL 2 GLYCOSYLASE (ECUDG) WITH A PROTEINACEOUS INHIBITOR. THE REMARK 1 TITL 3 STRUCTURE ELUCIDATION OF A PROKARYOTIC UDG. REMARK 1 REF NUCLEIC ACIDS RES. V. 26 4880 1998 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 9776748 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 39662 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) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.160 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2114 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2699 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE SET COUNT : 154 REMARK 3 BIN FREE R VALUE : 0.2210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1691 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 291 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : 0.75000 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): 0.054 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.052 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.870 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1824 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1726 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2508 ; 1.997 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3959 ; 0.971 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 237 ; 6.061 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;36.881 ;21.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 255 ;11.171 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;19.942 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 271 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2129 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 433 ; 0.002 ; 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): 931 ; 3.360 ; 1.548 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 930 ; 3.357 ; 1.547 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1172 ; 4.006 ; 2.331 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1173 ; 4.006 ; 2.332 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 893 ; 3.886 ; 1.786 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 891 ; 3.878 ; 1.784 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1335 ; 4.751 ; 2.569 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2362 ; 5.415 ;14.845 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2187 ; 4.853 ;13.551 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3550 ; 4.922 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 60 ;28.703 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3725 ;12.945 ; 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 : 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 4WS5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000204305. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41836 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 39.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.47900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3A7N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE TRIHYDRATE, SODIUM REMARK 280 CACODYLATE TRIHYDRATE, PEG 8000, JEFFAMINE M-600, PH 6.5, REMARK 280 MICROBATCH, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 23.26000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.44000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.44000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.26000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.01000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 GLY A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 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 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 8 CG CD OE1 OE2 REMARK 470 ARG A 12 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 195 CG CD1 CD2 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 690 O HOH A 691 2.04 REMARK 500 O HOH A 581 O HOH A 639 2.05 REMARK 500 O HOH A 599 O HOH A 640 2.11 REMARK 500 O HOH A 605 O HOH A 669 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 535 O HOH A 678 4455 1.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 59 CG ASN A 59 ND2 0.151 REMARK 500 ARG A 141 CZ ARG A 141 NH2 -0.097 REMARK 500 SER A 193 CB SER A 193 OG -0.093 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 51 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 58 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 88 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 MET A 178 CB - CG - SD ANGL. DEV. = -22.0 DEGREES REMARK 500 MET A 178 CG - SD - CE ANGL. DEV. = 21.8 DEGREES REMARK 500 MET A 217 CG - SD - CE ANGL. DEV. = -9.8 DEGREES REMARK 500 ASP A 223 CB - CG - OD1 ANGL. DEV. = 5.5 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 GLN A 67 -65.77 -100.78 REMARK 500 PHE A 81 -23.60 76.40 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 5NU A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WRU RELATED DB: PDB REMARK 900 RELATED ID: 4WRV RELATED DB: PDB REMARK 900 RELATED ID: 4WRW RELATED DB: PDB REMARK 900 RELATED ID: 4WRX RELATED DB: PDB REMARK 900 RELATED ID: 4WRY RELATED DB: PDB REMARK 900 RELATED ID: 4WRZ RELATED DB: PDB REMARK 900 RELATED ID: 4WS0 RELATED DB: PDB REMARK 900 RELATED ID: 4WS1 RELATED DB: PDB REMARK 900 RELATED ID: 4WS2 RELATED DB: PDB REMARK 900 RELATED ID: 4WS3 RELATED DB: PDB REMARK 900 RELATED ID: 4WS4 RELATED DB: PDB REMARK 900 RELATED ID: 4WS6 RELATED DB: PDB REMARK 900 RELATED ID: 4WS7 RELATED DB: PDB REMARK 900 RELATED ID: 4WS8 RELATED DB: PDB DBREF 4WS5 A 1 227 UNP P9WFQ9 UNG_MYCTU 1 227 SEQADV 4WS5 MET A -10 UNP P9WFQ9 INITIATING METHIONINE SEQADV 4WS5 HIS A -9 UNP P9WFQ9 EXPRESSION TAG SEQADV 4WS5 HIS A -8 UNP P9WFQ9 EXPRESSION TAG SEQADV 4WS5 HIS A -7 UNP P9WFQ9 EXPRESSION TAG SEQADV 4WS5 HIS A -6 UNP P9WFQ9 EXPRESSION TAG SEQADV 4WS5 HIS A -5 UNP P9WFQ9 EXPRESSION TAG SEQADV 4WS5 HIS A -4 UNP P9WFQ9 EXPRESSION TAG SEQADV 4WS5 GLY A -3 UNP P9WFQ9 EXPRESSION TAG SEQADV 4WS5 MET A -2 UNP P9WFQ9 EXPRESSION TAG SEQADV 4WS5 ALA A -1 UNP P9WFQ9 EXPRESSION TAG SEQADV 4WS5 SER A 0 UNP P9WFQ9 EXPRESSION TAG SEQRES 1 A 238 MET HIS HIS HIS HIS HIS HIS GLY MET ALA SER MET THR SEQRES 2 A 238 ALA ARG PRO LEU SER GLU LEU VAL GLU ARG GLY TRP ALA SEQRES 3 A 238 ALA ALA LEU GLU PRO VAL ALA ASP GLN VAL ALA HIS MET SEQRES 4 A 238 GLY GLN PHE LEU ARG ALA GLU ILE ALA ALA GLY ARG ARG SEQRES 5 A 238 TYR LEU PRO ALA GLY SER ASN VAL LEU ARG ALA PHE THR SEQRES 6 A 238 PHE PRO PHE ASP ASN VAL ARG VAL LEU ILE VAL GLY GLN SEQRES 7 A 238 ASP PRO TYR PRO THR PRO GLY HIS ALA VAL GLY LEU SER SEQRES 8 A 238 PHE SER VAL ALA PRO ASP VAL ARG PRO TRP PRO ARG SER SEQRES 9 A 238 LEU ALA ASN ILE PHE ASP GLU TYR THR ALA ASP LEU GLY SEQRES 10 A 238 TYR PRO LEU PRO SER ASN GLY ASP LEU THR PRO TRP ALA SEQRES 11 A 238 GLN ARG GLY VAL LEU LEU LEU ASN ARG VAL LEU THR VAL SEQRES 12 A 238 ARG PRO SER ASN PRO ALA SER HIS ARG GLY LYS GLY TRP SEQRES 13 A 238 GLU ALA VAL THR GLU CYS ALA ILE ARG ALA LEU ALA ALA SEQRES 14 A 238 ARG ALA ALA PRO LEU VAL ALA ILE LEU TRP GLY ARG ASP SEQRES 15 A 238 ALA SER THR LEU LYS PRO MET LEU ALA ALA GLY ASN CYS SEQRES 16 A 238 VAL ALA ILE GLU SER PRO HIS PRO SER PRO LEU SER ALA SEQRES 17 A 238 SER ARG GLY PHE PHE GLY SER ARG PRO PHE SER ARG ALA SEQRES 18 A 238 ASN GLU LEU LEU VAL GLY MET GLY ALA GLU PRO ILE ASP SEQRES 19 A 238 TRP ARG LEU PRO HET 5NU A 301 11 HET CL A 302 1 HET CL A 303 1 HETNAM 5NU 5-NITROURACIL HETNAM CL CHLORIDE ION FORMUL 2 5NU C4 H3 N3 O4 FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *291(H2 O) HELIX 1 AA1 PRO A 5 VAL A 10 1 6 HELIX 2 AA2 GLU A 11 LEU A 18 1 8 HELIX 3 AA3 VAL A 21 GLY A 39 1 19 HELIX 4 AA4 ALA A 45 VAL A 49 5 5 HELIX 5 AA5 LEU A 50 PHE A 55 5 6 HELIX 6 AA6 PRO A 56 VAL A 60 5 5 HELIX 7 AA7 PRO A 91 GLY A 106 1 16 HELIX 8 AA8 LEU A 115 ARG A 121 1 7 HELIX 9 AA9 GLY A 144 ARG A 159 1 16 HELIX 10 AB1 GLY A 169 THR A 174 1 6 HELIX 11 AB2 LEU A 175 ALA A 180 5 6 HELIX 12 AB3 ARG A 205 MET A 217 1 13 SHEET 1 AA1 4 VAL A 123 ASN A 127 0 SHEET 2 AA1 4 VAL A 62 GLY A 66 1 N VAL A 62 O LEU A 124 SHEET 3 AA1 4 LEU A 163 TRP A 168 1 O ILE A 166 N LEU A 63 SHEET 4 AA1 4 CYS A 184 SER A 189 1 O ILE A 187 N LEU A 167 CISPEP 1 LEU A 43 PRO A 44 0 -8.42 CISPEP 2 ARG A 88 PRO A 89 0 -16.54 SITE 1 AC1 13 GLY A 66 GLN A 67 ASP A 68 TYR A 70 SITE 2 AC1 13 SER A 80 PHE A 81 SER A 93 ASN A 127 SITE 3 AC1 13 HIS A 191 HOH A 542 HOH A 559 HOH A 598 SITE 4 AC1 13 HOH A 650 SITE 1 AC2 4 ARG A 41 ARG A 133 HOH A 612 HOH A 644 SITE 1 AC3 3 TYR A 107 ILE A 222 TRP A 224 CRYST1 46.520 60.020 74.880 90.00 90.00 90.00 P 21 21 21 4 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 0.021496 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013355 0.00000