HEADER HYDROLASE 11-APR-11 2YG9 TITLE STRUCTURE OF AN UNUSUAL 3-METHYLADENINE DNA GLYCOSYLASE II (ALKA) FROM TITLE 2 DEINOCOCCUS RADIODURANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-3-METHYLADENINE GLYCOSIDASE II, PUTATIVE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 GENE: DR_2584; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: CODONPLUS KEYWDS HYDROLASE, DNA REPAIR EXPDTA X-RAY DIFFRACTION AUTHOR E.MOE,D.R.HALL,I.LEIROS,V.TALSTAD,J.TIMMINS,S.MCSWEENEY REVDAT 5 20-DEC-23 2YG9 1 REMARK LINK REVDAT 4 05-DEC-18 2YG9 1 TITLE COMPND SOURCE AUTHOR REVDAT 4 2 1 JRNL DBREF REVDAT 3 20-JUN-12 2YG9 1 JRNL REVDAT 2 30-MAY-12 2YG9 1 JRNL REMARK VERSN HETSYN REVDAT 1 20-APR-11 2YG9 0 JRNL AUTH E.MOE,D.R.HALL,I.LEIROS,V.T.MONSEN,J.TIMMINS,S.MCSWEENEY JRNL TITL STRUCTURE-FUNCTION STUDIES OF AN UNUSUAL 3-METHYLADENINE DNA JRNL TITL 2 GLYCOSYLASE II (ALKA) FROM DEINOCOCCUS RADIODURANS. JRNL REF ACTA CRYSTALLOGR. D BIOL. V. 68 703 2012 JRNL REF 2 CRYSTALLOGR. JRNL REFN ESSN 1399-0047 JRNL PMID 22683793 JRNL DOI 10.1107/S090744491200947X REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 33988 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1802 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2533 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3073 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 612 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.04000 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): 0.150 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.152 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.454 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3207 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2193 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4391 ; 1.476 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5316 ; 1.017 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 425 ; 4.817 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;38.507 ;22.109 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 478 ;14.195 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;16.673 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 497 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3643 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 665 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 720 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2272 ; 0.204 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1568 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1683 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 372 ; 0.188 ; 0.200 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): 22 ; 0.259 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 99 ; 0.323 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 35 ; 0.215 ; 0.200 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): 2619 ; 1.013 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 842 ; 0.212 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3314 ; 1.280 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1296 ; 2.343 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1070 ; 3.528 ; 4.500 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 : 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 2YG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-APR-11. REMARK 100 THE DEPOSITION ID IS D_1290048003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND 111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35790 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 42.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2YG8 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 UL DROPS OF 10 MG/ML PROTEIN MIXED REMARK 280 WITH A SOLUTION CONTAINING 1 M LICL2, 0.1 M MES PH 6.0 AND 10% REMARK 280 PEG6000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 54.15550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.68600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.15550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.68600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 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 HOH B2104 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 1 REMARK 465 ARG A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 ALA A 5 REMARK 465 LEU A 6 REMARK 465 HIS A 7 REMARK 465 GLN A 8 REMARK 465 ASN A 9 REMARK 465 ARG A 10 REMARK 465 ARG A 11 REMARK 465 VAL A 12 REMARK 465 THR A 13 REMARK 465 LEU A 14 REMARK 465 PRO A 15 REMARK 465 SER A 16 REMARK 465 VAL A 17 REMARK 465 PRO A 18 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 GLY B 3 REMARK 465 GLY B 4 REMARK 465 ALA B 5 REMARK 465 LEU B 6 REMARK 465 HIS B 7 REMARK 465 GLN B 8 REMARK 465 ASN B 9 REMARK 465 ARG B 10 REMARK 465 ARG B 11 REMARK 465 VAL B 12 REMARK 465 THR B 13 REMARK 465 LEU B 14 REMARK 465 PRO B 15 REMARK 465 SER B 16 REMARK 465 VAL B 17 REMARK 465 PRO B 18 REMARK 465 LEU B 19 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 B 135 CG ND1 CD2 CE1 NE2 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 O3 GOL A 1228 O HOH A 2322 2.12 REMARK 500 OD2 ASP B 105 O HOH B 2167 2.17 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 156 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 156 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 199 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 67 NE - CZ - NH1 ANGL. DEV. = 3.1 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 PRO A 202 31.79 -90.05 REMARK 500 PRO B 202 31.11 -93.39 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 A2040 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2052 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH B2040 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH B2041 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH B2096 DISTANCE = 6.09 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 NI A1229 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 35 ND1 REMARK 620 2 HOH A2049 O 83.4 REMARK 620 3 HOH A2290 O 115.0 99.2 REMARK 620 4 HOH A2324 O 103.7 158.0 96.4 REMARK 620 5 HOH A2325 O 142.4 68.9 94.8 94.6 REMARK 620 6 NI B1228 NI 126.0 102.6 116.7 56.3 43.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1228 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2324 O REMARK 620 2 HOH A2325 O 87.6 REMARK 620 3 HIS B 35 ND1 120.9 120.7 REMARK 620 4 HOH B2048 O 59.8 140.2 68.0 REMARK 620 5 HOH B2260 O 110.3 93.0 117.6 118.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1226 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1227 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1226 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1227 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1228 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1228 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1229 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YG8 RELATED DB: PDB REMARK 900 STRUCTURE OF AN UNUSUAL 3-METHYLADENINE DNA GLYCOSYLASE II (ALKA) REMARK 900 FROM DEINOCOCCUS RADIODURANS DBREF 2YG9 A 1 225 UNP Q9RRB0 Q9RRB0_DEIRA 1 225 DBREF 2YG9 B 1 225 UNP Q9RRB0 Q9RRB0_DEIRA 1 225 SEQRES 1 A 225 MET ARG GLY GLY ALA LEU HIS GLN ASN ARG ARG VAL THR SEQRES 2 A 225 LEU PRO SER VAL PRO LEU PRO ALA VAL LEU PRO PRO LEU SEQRES 3 A 225 THR ASP HIS ALA GLY ALA VAL ALA HIS LEU SER ARG ASP SEQRES 4 A 225 PRO VAL LEU ALA GLN VAL THR SER LEU CYS GLY GLU LEU SEQRES 5 A 225 PRO VAL LEU ALA PRO THR PRO ASP PRO PHE GLY ARG LEU SEQRES 6 A 225 VAL ARG SER VAL ALA GLY GLN GLN LEU SER VAL LYS ALA SEQRES 7 A 225 ALA GLN ALA ILE TYR GLY ARG LEU GLU GLY LEU PRO GLY SEQRES 8 A 225 GLY VAL VAL PRO ALA ALA LEU LEU LYS VAL SER GLY ASP SEQRES 9 A 225 ASP LEU ARG GLY VAL GLY LEU SER TRP ALA LYS VAL ARG SEQRES 10 A 225 THR VAL GLN ALA ALA ALA ALA ALA ALA VAL SER GLY GLN SEQRES 11 A 225 ILE ASP PHE ALA HIS LEU SER GLY GLN PRO ASP GLU LEU SEQRES 12 A 225 VAL ILE ALA GLU LEU VAL GLN LEU PRO GLY ILE GLY ARG SEQRES 13 A 225 TRP THR ALA GLU MET PHE LEU LEU PHE ALA LEU ALA ARG SEQRES 14 A 225 PRO ASP VAL PHE SER SER GLY ASP LEU ALA LEU ARG GLN SEQRES 15 A 225 GLY VAL GLU ARG LEU TYR PRO GLY GLU ASP TRP ARG ASP SEQRES 16 A 225 VAL THR ALA ARG TRP ALA PRO TYR ARG SER LEU ALA SER SEQRES 17 A 225 ARG TYR LEU TRP ALA ASN SER ALA ARG MET GLN ALA GLY SEQRES 18 A 225 GLY ALA PRO LEU SEQRES 1 B 225 MET ARG GLY GLY ALA LEU HIS GLN ASN ARG ARG VAL THR SEQRES 2 B 225 LEU PRO SER VAL PRO LEU PRO ALA VAL LEU PRO PRO LEU SEQRES 3 B 225 THR ASP HIS ALA GLY ALA VAL ALA HIS LEU SER ARG ASP SEQRES 4 B 225 PRO VAL LEU ALA GLN VAL THR SER LEU CYS GLY GLU LEU SEQRES 5 B 225 PRO VAL LEU ALA PRO THR PRO ASP PRO PHE GLY ARG LEU SEQRES 6 B 225 VAL ARG SER VAL ALA GLY GLN GLN LEU SER VAL LYS ALA SEQRES 7 B 225 ALA GLN ALA ILE TYR GLY ARG LEU GLU GLY LEU PRO GLY SEQRES 8 B 225 GLY VAL VAL PRO ALA ALA LEU LEU LYS VAL SER GLY ASP SEQRES 9 B 225 ASP LEU ARG GLY VAL GLY LEU SER TRP ALA LYS VAL ARG SEQRES 10 B 225 THR VAL GLN ALA ALA ALA ALA ALA ALA VAL SER GLY GLN SEQRES 11 B 225 ILE ASP PHE ALA HIS LEU SER GLY GLN PRO ASP GLU LEU SEQRES 12 B 225 VAL ILE ALA GLU LEU VAL GLN LEU PRO GLY ILE GLY ARG SEQRES 13 B 225 TRP THR ALA GLU MET PHE LEU LEU PHE ALA LEU ALA ARG SEQRES 14 B 225 PRO ASP VAL PHE SER SER GLY ASP LEU ALA LEU ARG GLN SEQRES 15 B 225 GLY VAL GLU ARG LEU TYR PRO GLY GLU ASP TRP ARG ASP SEQRES 16 B 225 VAL THR ALA ARG TRP ALA PRO TYR ARG SER LEU ALA SER SEQRES 17 B 225 ARG TYR LEU TRP ALA ASN SER ALA ARG MET GLN ALA GLY SEQRES 18 B 225 GLY ALA PRO LEU HET CL A1226 1 HET CL A1227 1 HET GOL A1228 6 HET NI A1229 1 HET CL B1226 1 HET CL B1227 1 HET NI B1228 1 HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM NI NICKEL (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CL 4(CL 1-) FORMUL 5 GOL C3 H8 O3 FORMUL 6 NI 2(NI 2+) FORMUL 10 HOH *612(H2 O) HELIX 1 1 HIS A 29 SER A 37 1 9 HELIX 2 2 ASP A 39 GLY A 50 1 12 HELIX 3 3 ASP A 60 GLN A 72 1 13 HELIX 4 4 SER A 75 GLY A 88 1 14 HELIX 5 5 VAL A 94 LEU A 99 1 6 HELIX 6 6 SER A 102 VAL A 109 1 8 HELIX 7 7 SER A 112 SER A 128 1 17 HELIX 8 8 ASP A 132 LEU A 136 5 5 HELIX 9 9 PRO A 140 GLN A 150 1 11 HELIX 10 10 GLY A 155 ALA A 166 1 12 HELIX 11 11 ASP A 177 TYR A 188 1 12 HELIX 12 12 ASP A 192 ALA A 201 1 10 HELIX 13 13 TYR A 203 ALA A 220 1 18 HELIX 14 14 HIS B 29 SER B 37 1 9 HELIX 15 15 ASP B 39 GLY B 50 1 12 HELIX 16 16 ASP B 60 GLN B 72 1 13 HELIX 17 17 SER B 75 GLY B 88 1 14 HELIX 18 18 VAL B 94 LEU B 99 1 6 HELIX 19 19 SER B 102 VAL B 109 1 8 HELIX 20 20 SER B 112 SER B 128 1 17 HELIX 21 21 ASP B 132 GLN B 139 5 8 HELIX 22 22 PRO B 140 GLN B 150 1 11 HELIX 23 23 GLY B 155 ALA B 166 1 12 HELIX 24 24 ASP B 177 TYR B 188 1 12 HELIX 25 25 ASP B 192 ARG B 199 1 8 HELIX 26 26 TYR B 203 ALA B 220 1 18 LINK ND1 HIS A 35 NI NI A1229 1555 1555 2.49 LINK NI NI A1229 O HOH A2049 1555 1555 2.40 LINK NI NI A1229 O HOH A2290 1555 1555 2.46 LINK NI NI A1229 O HOH A2324 1555 1555 2.22 LINK NI NI A1229 O HOH A2325 1555 1555 2.49 LINK NI NI A1229 NI NI B1228 1555 1555 3.24 LINK O HOH A2324 NI NI B1228 1555 1555 2.73 LINK O HOH A2325 NI NI B1228 1555 1555 2.25 LINK ND1 HIS B 35 NI NI B1228 1555 1555 2.75 LINK NI NI B1228 O HOH B2048 1555 1555 2.69 LINK NI NI B1228 O HOH B2260 1555 1555 2.31 CISPEP 1 ALA A 201 PRO A 202 0 3.08 CISPEP 2 ALA B 201 PRO B 202 0 5.60 SITE 1 AC1 4 GOL A1228 GLY B 110 SER B 112 LYS B 115 SITE 1 AC2 2 GLY B 155 THR B 158 SITE 1 AC3 5 GLY A 110 SER A 112 LYS A 115 HOH A2078 SITE 2 AC3 5 HOH A2199 SITE 1 AC4 2 GLY A 155 THR A 158 SITE 1 AC5 11 PRO A 40 VAL A 41 HOH A2062 HOH A2074 SITE 2 AC5 11 HOH A2322 HOH A2323 ARG B 107 SER B 112 SITE 3 AC5 11 TRP B 113 CL B1226 HOH B2176 SITE 1 AC6 6 NI A1229 HOH A2324 HOH A2325 HIS B 35 SITE 2 AC6 6 HOH B2048 HOH B2260 SITE 1 AC7 7 HIS A 35 HOH A2049 HOH A2050 HOH A2290 SITE 2 AC7 7 HOH A2324 HOH A2325 NI B1228 CRYST1 108.311 51.372 90.039 90.00 99.71 90.00 C 1 2 1 8 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 0.009233 0.000000 0.001580 0.00000 SCALE2 0.000000 0.019466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011268 0.00000 MTRIX1 1 0.944560 -0.014900 0.328010 -21.21795 1 MTRIX2 1 -0.014740 -0.999890 -0.002950 -15.26268 1 MTRIX3 1 0.328020 -0.002050 -0.944670 124.27422 1