HEADER HYDROLASE/DNA 11-JAN-09 3FSQ OBSLTE 23-SEP-15 3FSQ 5DPK TITLE MUTY ADENINE GLYCOSYLASE BOUND TO A TRANSITION STATE ANALOG (1N) TITLE 2 PAIRED WITH D(8-OXOG) IN DUPLEXED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: A/G-SPECIFIC ADENINE GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*T*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3'; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: MUTY; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: DNA CHEMICALLY SYNTHESIZED WITH MODIFIED NUCLEOTIDE SOURCE 13 8-OXOG AT POSITION 6; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: DNA CHEMICALLY SYNTHESIZED WITH 1N TRANSITION STATE SOURCE 17 ANALOG AT POSITION 18 KEYWDS PROTEIN-DNA COMPLEX, DNA GLYCOSYLASE, TRANSITION STATE ANALOG, DNA KEYWDS 2 REPAIR, GLYCOSIDASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.L.O'SHEA,M.P.HORVATH,S.S.DAVID REVDAT 2 23-SEP-15 3FSQ 1 OBSLTE VERSN REVDAT 1 19-JAN-10 3FSQ 0 JRNL AUTH V.L.O'SHEA,S.CAO,J.L.RICHARDS,M.P.HORVATH,S.S.DAVID JRNL TITL STRUCTURAL ILLUMINATION OF A MUTY GLYCOSYLASE REACTION JRNL TITL 2 COORDINATE INTERMEDIATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 21062 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; SAME CROSS- REMARK 3 VALIDATION DATA SET AS USED REMARK 3 FOR REFINEMENT OF PDB ID 3FSP REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1003 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2736 REMARK 3 BIN R VALUE (WORKING SET) : 0.3036 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.87 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 140 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2753 REMARK 3 NUCLEIC ACID ATOMS : 421 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 136 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.14410 REMARK 3 B22 (A**2) : 8.30080 REMARK 3 B33 (A**2) : -2.59960 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.37 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.132 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.651 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 6.183 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 7.913 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : FS4B.CIF REMARK 3 PARAMETER FILE 2 : 8OG_SMILES_FROM_OG1N23A.CIF REMARK 3 PARAMETER FILE 3 : NRI_SMILES_FROM_OG1N23A.CIF REMARK 3 PARAMETER FILE 4 : NRI.EDITS REMARK 3 PARAMETER FILE 5 : METAL_OG1N23A_26.EDITS REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : FS4B.CIF REMARK 3 TOPOLOGY FILE 2 : 8OG_SMILES_FROM_OG1N23A.CIF REMARK 3 TOPOLOGY FILE 3 : NRI_SMILES_FROM_OG1N23A.CIF REMARK 3 TOPOLOGY FILE 4 : NRI.EDITS REMARK 3 TOPOLOGY FILE 5 : METAL_OG1N23A_26.EDITS REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ACTIVE SITE RESIDUES AND DNA REMARK 3 NUCLEOTIDES REMOVED FROM MR SEARCH MODEL; TORSION ANGLE SIMULATED REMARK 3 ANNEALING, POSITIONAL, RESTRAINED INDIVIDUAL B-VALUE REFINEMENT; REMARK 3 MODEL ADJUSTMENTS IN CONTEXT OF SIGMA-A WEIGHTED COMPOSITE SA- REMARK 3 OMIT MAPS REMARK 4 REMARK 4 3FSQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-09. REMARK 100 THE RCSB ID CODE IS RCSB050995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 12.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11583 REMARK 200 MONOCHROMATOR : SI(111) CRYSTALS REMARK 200 OPTICS : KOHZU, SI(111) CRYSTALS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21114 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.44500 REMARK 200 R SYM FOR SHELL (I) : 0.44500 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ID 1RRQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MICRO-SEEDED, 0.5M CALCIUM ACETATE, REMARK 280 0.1M TRIS, 14% (W/V) PEG4000, 0.005M BETA-MERCAPTOETHANOL, 5% (W/ REMARK 280 V) ETHYLENE GLYCOL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K 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 18.89650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.29250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.25800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.29250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.89650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.25800 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ARG A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 ARG A 7 REMARK 465 TYR A 290 REMARK 465 GLY A 291 REMARK 465 LEU A 292 REMARK 465 GLN A 293 REMARK 465 VAL A 294 REMARK 465 GLY A 361 REMARK 465 VAL A 362 REMARK 465 ARG A 363 REMARK 465 PRO A 364 REMARK 465 PRO A 365 REMARK 465 PRO A 366 REMARK 465 DT C 12 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 LYS A 103 CE NZ REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 GLN A 172 CG CD OE1 NE2 REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 LYS A 230 CD CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 GLU A 248 CD OE1 OE2 REMARK 470 LYS A 279 CG CD CE NZ REMARK 470 GLN A 289 CB CG CD OE1 NE2 REMARK 470 GLU A 295 CB CG CD OE1 OE2 REMARK 470 GLU A 328 CG CD OE1 OE2 REMARK 470 GLU A 329 CG CD OE1 OE2 REMARK 470 ASP A 337 CG OD1 OD2 REMARK 470 NRI C 18 O1P 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 ALA A 10 NE2 GLN A 14 2.08 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 DA B 2 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA B 2 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT B 7 C1' - O4' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC C 16 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DC C 16 O4' - C1' - N1 ANGL. DEV. = 4.3 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 9 72.98 -68.40 REMARK 500 ARG A 11 -47.18 -172.53 REMARK 500 GLN A 14 -1.08 -58.61 REMARK 500 LEU A 17 -60.54 -92.04 REMARK 500 TYR A 88 69.64 35.68 REMARK 500 LYS A 103 -74.10 -86.33 REMARK 500 PRO A 111 150.82 -44.56 REMARK 500 SER A 118 2.72 -61.92 REMARK 500 PRO A 139 24.04 -73.53 REMARK 500 VAL A 197 -69.50 -96.97 REMARK 500 ARG A 202 68.08 34.68 REMARK 500 MET A 229 132.71 -35.87 REMARK 500 LYS A 230 -162.98 -55.46 REMARK 500 ASP A 274 -96.56 65.17 REMARK 500 ASP A 277 31.48 146.40 REMARK 500 THR A 297 -110.23 -104.52 REMARK 500 REMARK 500 REMARK: NULL 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 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 118 O REMARK 620 2 SER A 118 OG 69.3 REMARK 620 3 VAL A 123 O 97.4 105.4 REMARK 620 4 HOH A 405 O 147.0 79.3 100.3 REMARK 620 5 HOH C 493 O 136.9 150.9 86.0 72.3 REMARK 620 6 HOH A 427 O 70.1 138.7 73.2 142.0 70.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 400 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 198 SG REMARK 620 2 SF4 A 400 S1 134.0 REMARK 620 3 SF4 A 400 S2 97.5 112.5 REMARK 620 4 SF4 A 400 S4 112.9 92.6 105.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 400 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 SF4 A 400 S1 86.7 REMARK 620 3 SF4 A 400 S3 155.4 104.6 REMARK 620 4 SF4 A 400 S4 90.0 91.5 111.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 400 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 SF4 A 400 S2 112.9 REMARK 620 3 SF4 A 400 S3 104.8 102.9 REMARK 620 4 SF4 A 400 S4 121.0 102.3 111.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 400 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 214 SG REMARK 620 2 SF4 A 400 S1 94.5 REMARK 620 3 SF4 A 400 S2 139.0 108.4 REMARK 620 4 SF4 A 400 S3 105.1 100.3 103.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FSP RELATED DB: PDB REMARK 900 MUTY ADENINE GLYCOSYLASE IN COMPLEX WITH DNA CONTAINING THE REMARK 900 1N TRANSITION STATE ANALOG PAIRED WITH GUANINE AT 2.20 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 1RRQ RELATED DB: PDB REMARK 900 MUTY BOUND TO DNA WITH AN A:8-OXOG BASEPAIR, THE LESION REMARK 900 RECOGNITION COMPLEX REMARK 900 RELATED ID: 1RRS RELATED DB: PDB REMARK 900 MUTY BOUND TO DNA WITH AN ABASIC SITE REMARK 900 RELATED ID: 1VRL RELATED DB: PDB REMARK 900 MUTY BOUND TO DNA AND ADENINE FREE BASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 Author states that the reference sequence (UNP P83847) is based on REMARK 999 a catalytically inactive mutant MutY (D144N). The SEQRES record REMARK 999 represent the wild-type sequence. DBREF 3FSQ A 1 366 UNP P83847 P83847_BACST 1 366 SEQADV 3FSQ GLY A -2 UNP P83847 EXPRESSION TAG SEQADV 3FSQ SER A -1 UNP P83847 EXPRESSION TAG SEQADV 3FSQ HIS A 0 UNP P83847 EXPRESSION TAG SEQADV 3FSQ ASP A 144 UNP P83847 ASN 144 SEE REMARK 999 SEQRES 1 A 369 GLY SER HIS MET THR ARG GLU THR GLU ARG PHE PRO ALA SEQRES 2 A 369 ARG GLU PHE GLN ARG ASP LEU LEU ASP TRP PHE ALA ARG SEQRES 3 A 369 GLU ARG ARG ASP LEU PRO TRP ARG LYS ASP ARG ASP PRO SEQRES 4 A 369 TYR LYS VAL TRP VAL SER GLU VAL MET LEU GLN GLN THR SEQRES 5 A 369 ARG VAL GLU THR VAL ILE PRO TYR PHE GLU GLN PHE ILE SEQRES 6 A 369 ASP ARG PHE PRO THR LEU GLU ALA LEU ALA ASP ALA ASP SEQRES 7 A 369 GLU ASP GLU VAL LEU LYS ALA TRP GLU GLY LEU GLY TYR SEQRES 8 A 369 TYR SER ARG VAL ARG ASN LEU HIS ALA ALA VAL LYS GLU SEQRES 9 A 369 VAL LYS THR ARG TYR GLY GLY LYS VAL PRO ASP ASP PRO SEQRES 10 A 369 ASP GLU PHE SER ARG LEU LYS GLY VAL GLY PRO TYR THR SEQRES 11 A 369 VAL GLY ALA VAL LEU SER LEU ALA TYR GLY VAL PRO GLU SEQRES 12 A 369 PRO ALA VAL ASP GLY ASN VAL MET ARG VAL LEU SER ARG SEQRES 13 A 369 LEU PHE LEU VAL THR ASP ASP ILE ALA LYS PRO SER THR SEQRES 14 A 369 ARG LYS ARG PHE GLU GLN ILE VAL ARG GLU ILE MET ALA SEQRES 15 A 369 TYR GLU ASN PRO GLY ALA PHE ASN GLU ALA LEU ILE GLU SEQRES 16 A 369 LEU GLY ALA LEU VAL CYS THR PRO ARG ARG PRO SER CYS SEQRES 17 A 369 LEU LEU CYS PRO VAL GLN ALA TYR CYS GLN ALA PHE ALA SEQRES 18 A 369 GLU GLY VAL ALA GLU GLU LEU PRO VAL LYS MET LYS LYS SEQRES 19 A 369 THR ALA VAL LYS GLN VAL PRO LEU ALA VAL ALA VAL LEU SEQRES 20 A 369 ALA ASP ASP GLU GLY ARG VAL LEU ILE ARG LYS ARG ASP SEQRES 21 A 369 SER THR GLY LEU LEU ALA ASN LEU TRP GLU PHE PRO SER SEQRES 22 A 369 CYS GLU THR ASP GLY ALA ASP GLY LYS GLU LYS LEU GLU SEQRES 23 A 369 GLN MET VAL GLY GLU GLN TYR GLY LEU GLN VAL GLU LEU SEQRES 24 A 369 THR GLU PRO ILE VAL SER PHE GLU HIS ALA PHE SER HIS SEQRES 25 A 369 LEU VAL TRP GLN LEU THR VAL PHE PRO GLY ARG LEU VAL SEQRES 26 A 369 HIS GLY GLY PRO VAL GLU GLU PRO TYR ARG LEU ALA PRO SEQRES 27 A 369 GLU ASP GLU LEU LYS ALA TYR ALA PHE PRO VAL SER HIS SEQRES 28 A 369 GLN ARG VAL TRP ARG GLU TYR LYS GLU TRP ALA SER GLY SEQRES 29 A 369 VAL ARG PRO PRO PRO SEQRES 1 B 11 DA DA DG DA DC 8OG DT DG DG DA DC SEQRES 1 C 11 DT DG DT DC DC DA NRI DG DT DC DT MODRES 3FSQ 8OG B 6 DG HET 8OG B 6 23 HET NRI C 18 11 HET SF4 A 400 8 HET CA A 501 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM NRI PHOSPHORIC ACID MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL) HETNAM 2 NRI ESTER HETNAM SF4 IRON/SULFUR CLUSTER HETNAM CA CALCIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 3 NRI C5 H12 N O5 P FORMUL 4 SF4 FE4 S4 FORMUL 5 CA CA 2+ FORMUL 6 HOH *136(H2 O) HELIX 1 1 PRO A 9 ARG A 25 1 17 HELIX 2 2 LEU A 28 LYS A 32 5 5 HELIX 3 3 ASP A 35 LEU A 46 1 12 HELIX 4 4 ARG A 50 PHE A 65 1 16 HELIX 5 5 THR A 67 ASP A 73 1 7 HELIX 6 6 ASP A 75 LEU A 80 1 6 HELIX 7 7 LYS A 81 GLU A 84 5 4 HELIX 8 8 TYR A 89 ARG A 105 1 17 HELIX 9 9 ASP A 113 SER A 118 1 6 HELIX 10 10 GLY A 124 TYR A 136 1 13 HELIX 11 11 ASP A 144 PHE A 155 1 12 HELIX 12 12 SER A 165 MET A 178 1 14 HELIX 13 13 ASN A 182 VAL A 197 1 16 HELIX 14 14 CYS A 214 GLU A 219 1 6 HELIX 15 15 ASP A 277 GLY A 287 1 11 HELIX 16 16 PRO A 335 TYR A 342 5 8 HELIX 17 17 PRO A 345 ALA A 359 1 15 SHEET 1 A 4 SER A 270 GLU A 272 0 SHEET 2 A 4 LYS A 235 ASP A 246 -1 N ALA A 240 O CYS A 271 SHEET 3 A 4 LEU A 310 LEU A 321 1 O GLN A 313 N LEU A 239 SHEET 4 A 4 VAL A 301 ALA A 306 -1 N HIS A 305 O TRP A 312 SHEET 1 B 3 TRP A 266 GLU A 267 0 SHEET 2 B 3 VAL A 251 LYS A 255 -1 N ARG A 254 O GLU A 267 SHEET 3 B 3 TYR A 331 ALA A 334 -1 O ALA A 334 N VAL A 251 LINK O3' DC B 5 P 8OG B 6 1555 1555 1.59 LINK O3' 8OG B 6 P DT B 7 1555 1555 1.60 LINK O3' DA C 17 P NRI C 18 1555 1555 1.61 LINK O3' NRI C 18 P DG C 19 1555 1555 1.60 LINK O SER A 118 CA CA A 501 1555 1555 2.23 LINK OG SER A 118 CA CA A 501 1555 1555 2.30 LINK O VAL A 123 CA CA A 501 1555 1555 2.22 LINK SG CYS A 198 FE3 SF4 A 400 1555 1555 2.31 LINK SG CYS A 205 FE2 SF4 A 400 1555 1555 2.08 LINK SG CYS A 208 FE1 SF4 A 400 1555 1555 2.17 LINK SG CYS A 214 FE4 SF4 A 400 1555 1555 2.09 LINK CA CA A 501 O HOH A 405 1555 1555 2.63 LINK CA CA A 501 O HOH C 493 1555 1555 2.21 LINK CA CA A 501 O HOH A 427 1555 1555 2.29 CISPEP 1 LEU A 225 PRO A 226 0 -5.84 CISPEP 2 GLU A 329 PRO A 330 0 5.22 SITE 1 AC1 6 CYS A 198 PRO A 203 CYS A 205 CYS A 208 SITE 2 AC1 6 GLN A 211 CYS A 214 SITE 1 AC2 5 SER A 118 VAL A 123 HOH A 405 HOH A 427 SITE 2 AC2 5 HOH C 493 CRYST1 37.793 86.516 140.585 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 0.026460 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011559 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007113 0.00000