HEADER HYDROLASE 16-MAR-20 6M72 TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS MUTT1 IN COMPLEX WITH 8- TITLE 2 OXO-DGDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROLASE, NUDIX FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: MC2 155; SOURCE 5 GENE: MSMEG_2390; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JW0097 KEYWDS MSMUTT1, NUDIX HYDROLASE, HISTIDINE PHOSPHATASE DOMAIN, NUCLEOTIDE KEYWDS 2 POOL SANITATION ENZYME, 8-OXO-DGDP, MOLECULAR AGGREGATION, KEYWDS 3 PLASTICITY, ENZYME ACTION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.RAJ,S.KARTHIK,S.M.ARIF,U.VARSHNEY,M.VIJAYAN REVDAT 3 29-NOV-23 6M72 1 REMARK REVDAT 2 28-OCT-20 6M72 1 REMARK REVDAT 1 14-OCT-20 6M72 0 JRNL AUTH P.RAJ,S.KARTHIK,S.M.ARIF,U.VARSHNEY,M.VIJAYAN JRNL TITL PLASTICITY, LIGAND CONFORMATION AND ENZYME ACTION OF JRNL TITL 2 MYCOBACTERIUM SMEGMATIS MUTT1. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 76 982 2020 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 33021500 JRNL DOI 10.1107/S2059798320010992 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.M.ARIF,A.G.PATIL,U.VARSHNEY,M.VIJAYAN REMARK 1 TITL BIOCHEMICAL AND STRUCTURAL STUDIES OF MYCOBACTERIUM REMARK 1 TITL 2 SMEGMATIS MUTT1, A SANITIZATION ENZYME WITH UNUSUAL MODES OF REMARK 1 TITL 3 ASSOCIATION. REMARK 1 REF ACTA CRYSTALLOGR D STRUCT V. 73 349 2017 REMARK 1 REF 2 BIOL REMARK 1 REFN ISSN 2059-7983 REMARK 1 PMID 28375146 REMARK 1 DOI 10.1107/S2059798317002534 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.M.ARIF,U.VARSHNEY,M.VIJAYAN REMARK 1 TITL HYDROLYSIS OF DIADENOSINE POLYPHOSPHATES. EXPLORATION OF AN REMARK 1 TITL 2 ADDITIONAL ROLE OF MYCOBACTERIUM SMEGMATIS MUTT1. REMARK 1 REF J. STRUCT. BIOL. V. 199 165 2017 REMARK 1 REFN ESSN 1095-8657 REMARK 1 PMID 28705712 REMARK 1 DOI 10.1016/J.JSB.2017.07.002 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 40547 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2142 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2922 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 189 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2299 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 377 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.79000 REMARK 3 B22 (A**2) : 0.25000 REMARK 3 B33 (A**2) : 0.54000 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): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.436 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2467 ; 0.015 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2300 ; 0.034 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3373 ; 1.851 ; 1.663 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5311 ; 2.322 ; 1.586 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 307 ; 6.326 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 145 ;28.217 ;20.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 412 ;15.641 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;16.455 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 310 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2803 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 551 ; 0.015 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: INDIVIDUAL ISOTROPIC B-FACTOR REMARK 3 REFINEMENT REMARK 4 REMARK 4 6M72 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016195. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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) : 0.95372 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42971 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14900 REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.54600 REMARK 200 R SYM FOR SHELL (I) : 0.54600 REMARK 200 FOR SHELL : 1.300 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: 5GG5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE, 30% W/V PEG 4000, PH 4.6, MICROBATCH, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 96.01450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 96.01450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.54500 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 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 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 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 MET A 2 REMARK 465 PRO A 3 REMARK 465 VAL A 4 REMARK 465 ASP A 5 REMARK 465 ASP A 6 REMARK 465 LEU A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 REMARK 465 ILE A 10 REMARK 465 PRO A 11 REMARK 465 LEU A 12 REMARK 465 SER A 13 REMARK 465 LYS A 14 REMARK 465 ASP A 15 REMARK 465 THR A 16 REMARK 465 THR A 17 REMARK 465 GLU A 18 REMARK 465 LYS A 19 REMARK 465 SER A 20 REMARK 465 LYS A 21 REMARK 465 GLU A 37 REMARK 465 HIS A 38 REMARK 465 GLY A 39 REMARK 465 GLY A 40 REMARK 465 THR A 41 REMARK 465 THR A 42 REMARK 465 GLY A 43 REMARK 465 HIS A 44 REMARK 465 PRO A 45 REMARK 465 ALA A 46 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 289 CZ 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 GLU A 85 CD GLU A 85 OE1 -0.074 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 173 31.23 -142.12 REMARK 500 THR A 270 -158.10 -144.22 REMARK 500 ASN A 295 30.59 -152.36 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 874 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 875 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 876 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A 877 DISTANCE = 6.72 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 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 65 O REMARK 620 2 GLU A 85 OE2 83.9 REMARK 620 3 GLU A 127 OE2 131.8 47.9 REMARK 620 4 HOH A 525 O 93.7 174.8 134.4 REMARK 620 5 HOH A 609 O 80.4 69.4 83.8 105.7 REMARK 620 6 HOH A 799 O 95.5 99.5 91.1 85.3 168.4 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 8GD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue POP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6M6Y RELATED DB: PDB REMARK 900 6M6Y CONTAINS THE SAME PROTEIN COMPLEXED WITH 8-OXO-DGTP DBREF 6M72 A 1 322 UNP A0QUZ2 A0QUZ2_MYCS2 1 322 SEQADV 6M72 MET A -19 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 GLY A -18 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 SER A -17 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 SER A -16 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 HIS A -15 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 HIS A -14 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 HIS A -13 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 HIS A -12 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 HIS A -11 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 HIS A -10 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 SER A -9 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 SER A -8 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 GLY A -7 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 LEU A -6 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 VAL A -5 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 PRO A -4 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 ARG A -3 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 GLY A -2 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 SER A -1 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M72 HIS A 0 UNP A0QUZ2 EXPRESSION TAG SEQRES 1 A 342 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 342 LEU VAL PRO ARG GLY SER HIS MET MET PRO VAL ASP ASP SEQRES 3 A 342 LEU GLN GLU ILE PRO LEU SER LYS ASP THR THR GLU LYS SEQRES 4 A 342 SER LYS HIS THR VAL ARG ALA ALA GLY ALA VAL LEU TRP SEQRES 5 A 342 ARG ASP ALA SER GLU HIS GLY GLY THR THR GLY HIS PRO SEQRES 6 A 342 ALA THR VAL GLU VAL ALA VAL ILE HIS ARG PRO ARG TYR SEQRES 7 A 342 ASP ASP TRP SER LEU PRO LYS GLY LYS LEU ASP GLN GLY SEQRES 8 A 342 GLU THR GLU PRO VAL ALA ALA ALA ARG GLU ILE HIS GLU SEQRES 9 A 342 GLU THR GLY HIS THR ALA VAL LEU GLY ARG ARG LEU GLY SEQRES 10 A 342 ARG VAL THR TYR PRO ILE PRO GLN GLY THR LYS ARG VAL SEQRES 11 A 342 TRP TYR TRP ALA ALA LYS SER THR GLY GLY ASP PHE SER SEQRES 12 A 342 PRO ASN ASP GLU VAL ASP LYS LEU VAL TRP LEU PRO VAL SEQRES 13 A 342 ASP ALA ALA MET ASP GLN LEU GLN TYR PRO ASP ASP ARG SEQRES 14 A 342 LYS VAL LEU ARG ARG PHE VAL LYS ARG PRO VAL ASP THR SEQRES 15 A 342 LYS THR VAL LEU VAL VAL ARG HIS GLY THR ALA GLY ARG SEQRES 16 A 342 ARG SER ARG TYR LYS GLY ASP ASP ARG LYS ARG PRO LEU SEQRES 17 A 342 ASP LYS ARG GLY ARG ALA GLN ALA GLU ALA LEU VAL ALA SEQRES 18 A 342 GLN LEU MET ALA PHE GLY ALA THR THR LEU TYR ALA ALA SEQRES 19 A 342 ASP ARG VAL ARG CYS HIS GLN THR ILE GLU PRO LEU ALA SEQRES 20 A 342 GLN GLU LEU ASP GLN LEU ILE HIS ASN GLU PRO LEU LEU SEQRES 21 A 342 THR GLU GLU ALA TYR ALA ALA ASP HIS LYS ALA ALA ARG SEQRES 22 A 342 LYS ARG LEU LEU GLU ILE ALA GLY ARG PRO GLY ASN PRO SEQRES 23 A 342 VAL ILE CYS THR GLN GLY LYS VAL ILE PRO GLY LEU ILE SEQRES 24 A 342 GLU TRP TRP CYS GLU ARG ALA LYS VAL ARG PRO GLU THR SEQRES 25 A 342 THR GLY ASN ARG LYS GLY SER THR TRP VAL LEU SER LEU SEQRES 26 A 342 SER ASP GLY GLU LEU VAL GLY ALA ASP TYR LEU SER PRO SEQRES 27 A 342 PRO ASP GLU LYS HET 8GD A 401 28 HET POP A 402 9 HET MG A 403 1 HETNAM 8GD 2'-DEOXY-8-OXOGUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) HETNAM POP PYROPHOSPHATE 2- HETNAM MG MAGNESIUM ION HETSYN 8GD 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-DIPHOSPHATE FORMUL 2 8GD C10 H15 N5 O11 P2 FORMUL 3 POP H2 O7 P2 2- FORMUL 4 MG MG 2+ FORMUL 5 HOH *377(H2 O) HELIX 1 AA1 THR A 73 GLY A 87 1 15 HELIX 2 AA2 PRO A 135 LEU A 143 1 9 HELIX 3 AA3 TYR A 145 LYS A 157 1 13 HELIX 4 AA4 ARG A 175 TYR A 179 5 5 HELIX 5 AA5 ASP A 182 ARG A 186 5 5 HELIX 6 AA6 ASP A 189 ALA A 205 1 17 HELIX 7 AA7 ARG A 216 ILE A 223 1 8 HELIX 8 AA8 ILE A 223 ASP A 231 1 9 HELIX 9 AA9 PRO A 238 LEU A 240 5 3 HELIX 10 AB1 THR A 241 ASP A 248 1 8 HELIX 11 AB2 ASP A 248 ARG A 262 1 15 HELIX 12 AB3 VAL A 274 LYS A 287 1 14 SHEET 1 AA1 5 ASP A 60 SER A 62 0 SHEET 2 AA1 5 VAL A 48 ARG A 55 -1 N ILE A 53 O SER A 62 SHEET 3 AA1 5 THR A 23 ASP A 34 -1 N LEU A 31 O ALA A 51 SHEET 4 AA1 5 GLY A 106 GLY A 120 1 O THR A 107 N VAL A 24 SHEET 5 AA1 5 HIS A 88 ILE A 103 -1 N LEU A 96 O TYR A 112 SHEET 1 AA2 4 LYS A 65 LYS A 67 0 SHEET 2 AA2 4 THR A 23 ASP A 34 -1 N ALA A 27 O GLY A 66 SHEET 3 AA2 4 VAL A 48 ARG A 55 -1 O ALA A 51 N LEU A 31 SHEET 4 AA2 4 LYS A 130 LEU A 134 -1 O LEU A 134 N VAL A 50 SHEET 1 AA3 6 ILE A 234 GLU A 237 0 SHEET 2 AA3 6 THR A 210 ALA A 214 1 N LEU A 211 O HIS A 235 SHEET 3 AA3 6 PRO A 266 THR A 270 1 O CYS A 269 N ALA A 214 SHEET 4 AA3 6 LYS A 163 ARG A 169 1 N LEU A 166 O PRO A 266 SHEET 5 AA3 6 THR A 300 SER A 306 -1 O TRP A 301 N VAL A 167 SHEET 6 AA3 6 GLU A 309 LEU A 316 -1 O LEU A 316 N THR A 300 LINK O LYS A 65 MG MG A 403 1555 1555 2.44 LINK OE2 GLU A 85 MG MG A 403 1555 1555 2.40 LINK OE2 GLU A 127 MG MG A 403 1555 1555 3.00 LINK MG MG A 403 O HOH A 525 1555 1555 2.47 LINK MG MG A 403 O HOH A 609 1555 1555 2.38 LINK MG MG A 403 O HOH A 799 1555 1555 2.40 SITE 1 AC1 20 ARG A 55 ARG A 57 TYR A 58 LYS A 65 SITE 2 AC1 20 LYS A 67 TYR A 101 ILE A 103 LYS A 108 SITE 3 AC1 20 TYR A 145 ASP A 147 ASP A 148 HOH A 525 SITE 4 AC1 20 HOH A 528 HOH A 571 HOH A 600 HOH A 633 SITE 5 AC1 20 HOH A 637 HOH A 684 HOH A 738 HOH A 743 SITE 1 AC2 13 ARG A 169 HIS A 170 ARG A 176 ARG A 186 SITE 2 AC2 13 ARG A 218 GLU A 242 GLN A 271 GLY A 272 SITE 3 AC2 13 LYS A 297 HOH A 574 HOH A 598 HOH A 638 SITE 4 AC2 13 HOH A 667 SITE 1 AC3 6 LYS A 65 GLU A 85 GLU A 127 HOH A 525 SITE 2 AC3 6 HOH A 609 HOH A 799 CRYST1 192.029 37.090 44.650 90.00 90.00 90.00 P 21 21 2 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 0.005208 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022396 0.00000