HEADER HYDROLASE 25-OCT-14 4WS8
TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS URACIL-DNA GLYCOSYLASE
TITLE 2 IN COMPLEX WITH 2-THIOURACIL, FORM V
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 4WS8 1 REMARK
REVDAT 3 22-NOV-17 4WS8 1 SOURCE REMARK
REVDAT 2 22-JUL-15 4WS8 1 JRNL
REVDAT 1 15-JUL-15 4WS8 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) : 40.69
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 39146
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) : 0.134
REMARK 3 R VALUE (WORKING SET) : 0.132
REMARK 3 FREE R VALUE : 0.168
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2072
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) : 2843
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2610
REMARK 3 BIN FREE R VALUE SET COUNT : 158
REMARK 3 BIN FREE R VALUE : 0.3120
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1750
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 9
REMARK 3 SOLVENT ATOMS : 211
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.46
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.91000
REMARK 3 B22 (A**2) : -0.49000
REMARK 3 B33 (A**2) : -0.42000
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): 0.060
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.401
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978
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): 1944 ; 0.012 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 1848 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2678 ; 1.631 ; 1.975
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4237 ; 0.877 ; 3.001
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 258 ; 5.640 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 81 ;36.317 ;21.358
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 281 ;12.286 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;19.626 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 286 ; 0.094 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2295 ; 0.001 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 474 ; 0.000 ; 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): 987 ; 1.776 ; 1.322
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 986 ; 1.763 ; 1.320
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1251 ; 2.294 ; 1.999
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1252 ; 2.293 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 957 ; 3.630 ; 1.678
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 958 ; 3.629 ; 1.678
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1423 ; 3.939 ; 2.387
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2419 ; 4.697 ;12.493
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2338 ; 4.121 ;11.956
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3792 ; 2.472 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 82 ;34.478 ; 5.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3859 ; 9.801 ; 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 4WS8 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_1000204317.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-DEC-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.6
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) : 0.978565
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 : 41291
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400
REMARK 200 RESOLUTION RANGE LOW (A) : 40.690
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 6.000
REMARK 200 R MERGE (I) : 0.10300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.3000
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 (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 6.00
REMARK 200 R MERGE FOR SHELL (I) : 0.92300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900
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 (%): 40.13
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE, SODIUM CITRATE
REMARK 280 TRIBASIC DIHYDRATE, PEG 4000, PH 5.6, MICROBATCH, TEMPERATURE
REMARK 280 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 18.53000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.03000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.53500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.03000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.53000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.53500
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 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 -4 CG ND1 CD2 CE1 NE2
REMARK 470 THR A 2 OG1 CG2
REMARK 470 ARG A 170 CG CD NE CZ NH1 NH2
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 453 O HOH A 478 2.13
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 41 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 ARG A 51 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 ARG A 61 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = 3.4 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 PHE A 81 -18.02 71.63
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 TUL 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 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: 4WS5 RELATED DB: PDB
REMARK 900 RELATED ID: 4WS6 RELATED DB: PDB
REMARK 900 RELATED ID: 4WS7 RELATED DB: PDB
DBREF 4WS8 A 1 227 UNP P9WFQ9 UNG_MYCTU 1 227
SEQADV 4WS8 MET A -10 UNP P9WFQ9 INITIATING METHIONINE
SEQADV 4WS8 HIS A -9 UNP P9WFQ9 EXPRESSION TAG
SEQADV 4WS8 HIS A -8 UNP P9WFQ9 EXPRESSION TAG
SEQADV 4WS8 HIS A -7 UNP P9WFQ9 EXPRESSION TAG
SEQADV 4WS8 HIS A -6 UNP P9WFQ9 EXPRESSION TAG
SEQADV 4WS8 HIS A -5 UNP P9WFQ9 EXPRESSION TAG
SEQADV 4WS8 HIS A -4 UNP P9WFQ9 EXPRESSION TAG
SEQADV 4WS8 GLY A -3 UNP P9WFQ9 EXPRESSION TAG
SEQADV 4WS8 MET A -2 UNP P9WFQ9 EXPRESSION TAG
SEQADV 4WS8 ALA A -1 UNP P9WFQ9 EXPRESSION TAG
SEQADV 4WS8 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 TUL A 301 16
HET CL A 302 1
HETNAM TUL 2-THIOXO-2,3-DIHYDROPYRIMIDIN-4(1H)-ONE
HETNAM CL CHLORIDE ION
FORMUL 2 TUL C4 H4 N2 O S
FORMUL 3 CL CL 1-
FORMUL 4 HOH *211(H2 O)
HELIX 1 AA1 GLY A -3 ARG A 4 1 8
HELIX 2 AA2 PRO A 5 LEU A 9 5 5
HELIX 3 AA3 GLU A 11 LEU A 18 1 8
HELIX 4 AA4 VAL A 21 ALA A 38 1 18
HELIX 5 AA5 ALA A 45 VAL A 49 5 5
HELIX 6 AA6 LEU A 50 PHE A 55 5 6
HELIX 7 AA7 PRO A 56 VAL A 60 5 5
HELIX 8 AA8 PRO A 91 GLY A 106 1 16
HELIX 9 AA9 LEU A 115 ARG A 121 1 7
HELIX 10 AB1 GLY A 144 ARG A 159 1 16
HELIX 11 AB2 ASP A 171 THR A 174 5 4
HELIX 12 AB3 LEU A 175 GLY A 182 1 8
HELIX 13 AB4 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 VAL A 164 TRP A 168 1 O ILE A 166 N LEU A 63
SHEET 4 AA1 4 VAL A 185 SER A 189 1 O ILE A 187 N LEU A 167
CISPEP 1 LEU A 43 PRO A 44 0 -4.69
CISPEP 2 ARG A 88 PRO A 89 0 -3.64
CISPEP 3 ARG A 88 PRO A 89 0 -8.00
SITE 1 AC1 9 GLN A 67 ASP A 68 TYR A 70 SER A 80
SITE 2 AC1 9 PHE A 81 ASN A 127 HIS A 191 HOH A 493
SITE 3 AC1 9 HOH A 542
SITE 1 AC2 3 ALA A -1 ARG A 33 ARG A 209
CRYST1 37.060 45.070 122.060 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 0.026983 0.000000 0.000000 0.00000
SCALE2 0.000000 0.022188 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008193 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
