HEADER HYDROLASE/DNA 25-OCT-11 3UBY TITLE CRYSTAL STRUCTURE OF HUMAN ALKLYADENINE DNA GLYCOSYLASE IN A LOWER AND TITLE 2 HIGHER-AFFINITY COMPLEX WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-3-METHYLADENINE GLYCOSYLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DELTA79AAG; COMPND 5 SYNONYM: 3-ALKYLADENINE DNA GLYCOSYLASE, 3-METHYLADENINE DNA COMPND 6 GLYCOSIDASE, ADPG, N-METHYLPURINE-DNA GLYCOSYLASE; COMPND 7 EC: 3.2.2.21; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3'); COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MPG, AAG, ANPG, MID1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS ALKYLADENINE DNA GLYCOSYLASE FOLD, AAG, DNA REPAIR, DNA BINDING, KEYWDS 2 NUCLEUS, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.W.SETSER,G.M.LINGARAJU,C.A.DAVIS,L.D.SAMSON,C.L.DRENNAN REVDAT 4 25-JAN-12 3UBY 1 JRNL REVDAT 3 18-JAN-12 3UBY 1 HETATM REVDAT 2 11-JAN-12 3UBY 1 JRNL REVDAT 1 28-DEC-11 3UBY 0 JRNL AUTH J.W.SETSER,G.M.LINGARAJU,C.A.DAVIS,L.D.SAMSON,C.L.DRENNAN JRNL TITL SEARCHING FOR DNA LESIONS: STRUCTURAL EVIDENCE FOR LOWER- JRNL TITL 2 AND HIGHER-AFFINITY DNA BINDING CONFORMATIONS OF HUMAN JRNL TITL 3 ALKYLADENINE DNA GLYCOSYLASE. JRNL REF BIOCHEMISTRY V. 51 382 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22148158 JRNL DOI 10.1021/BI201484K REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 25556 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1375 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1833 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 99 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2967 REMARK 3 NUCLEIC ACID ATOMS : 354 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : 0.41000 REMARK 3 B33 (A**2) : -0.82000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.208 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.087 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3429 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4709 ; 1.104 ; 2.112 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 376 ; 5.055 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;31.096 ;22.029 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 504 ;14.599 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;14.494 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 513 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2502 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1900 ; 2.610 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3031 ; 3.499 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1529 ; 5.260 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1678 ; 6.684 ; 4.500 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 80 A 200 REMARK 3 RESIDUE RANGE : A 209 A 264 REMARK 3 RESIDUE RANGE : A 268 A 290 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6984 -5.0095 21.4544 REMARK 3 T TENSOR REMARK 3 T11: 0.2203 T22: 0.0209 REMARK 3 T33: 0.1267 T12: 0.0217 REMARK 3 T13: -0.0121 T23: -0.0225 REMARK 3 L TENSOR REMARK 3 L11: 1.8175 L22: 1.8300 REMARK 3 L33: 2.5151 L12: -0.7560 REMARK 3 L13: -0.8565 L23: 0.6659 REMARK 3 S TENSOR REMARK 3 S11: 0.0444 S12: 0.0808 S13: -0.0785 REMARK 3 S21: 0.1421 S22: -0.1046 S23: 0.0499 REMARK 3 S31: -0.0796 S32: 0.0603 S33: 0.0602 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 5 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 80 B 130 REMARK 3 RESIDUE RANGE : B 144 B 160 REMARK 3 RESIDUE RANGE : B 166 B 198 REMARK 3 RESIDUE RANGE : B 208 B 262 REMARK 3 RESIDUE RANGE : B 274 B 289 REMARK 3 ORIGIN FOR THE GROUP (A): -15.1881 -26.4475 -1.8766 REMARK 3 T TENSOR REMARK 3 T11: 0.1001 T22: 0.1592 REMARK 3 T33: 0.1279 T12: 0.0275 REMARK 3 T13: 0.0268 T23: -0.0474 REMARK 3 L TENSOR REMARK 3 L11: 1.7615 L22: 3.1614 REMARK 3 L33: 3.6281 L12: -0.8740 REMARK 3 L13: 0.8017 L23: -0.6637 REMARK 3 S TENSOR REMARK 3 S11: -0.0657 S12: 0.1840 S13: 0.0425 REMARK 3 S21: -0.1014 S22: 0.1151 S23: -0.0269 REMARK 3 S31: 0.0369 S32: -0.1413 S33: -0.0493 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 11 REMARK 3 ORIGIN FOR THE GROUP (A): 7.7356 1.8047 40.2028 REMARK 3 T TENSOR REMARK 3 T11: 0.4785 T22: 0.4773 REMARK 3 T33: 0.2180 T12: -0.0197 REMARK 3 T13: -0.0250 T23: 0.0084 REMARK 3 L TENSOR REMARK 3 L11: 0.5437 L22: 1.8201 REMARK 3 L33: 2.8380 L12: 0.9939 REMARK 3 L13: 1.2020 L23: 2.2202 REMARK 3 S TENSOR REMARK 3 S11: 0.0469 S12: -0.0752 S13: 0.0119 REMARK 3 S21: 0.1083 S22: -0.1109 S23: 0.0343 REMARK 3 S31: 0.1071 S32: 0.1185 S33: 0.0641 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 8 REMARK 3 ORIGIN FOR THE GROUP (A): 9.5881 9.3631 38.6698 REMARK 3 T TENSOR REMARK 3 T11: 0.2237 T22: 0.2337 REMARK 3 T33: 0.1711 T12: -0.0591 REMARK 3 T13: -0.0267 T23: -0.1381 REMARK 3 L TENSOR REMARK 3 L11: 1.8467 L22: 10.8793 REMARK 3 L33: 12.9283 L12: 0.5130 REMARK 3 L13: -2.3749 L23: -2.1692 REMARK 3 S TENSOR REMARK 3 S11: 0.0918 S12: -0.5275 S13: 0.3550 REMARK 3 S21: 0.1186 S22: 0.4908 S23: -0.4344 REMARK 3 S31: -0.3425 S32: 0.3405 S33: -0.5826 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3UBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-11. REMARK 100 THE RCSB ID CODE IS RCSB068561. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-06 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 : 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) : 1.116 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, DOUBLE MULTILAYER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26998 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 66.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: PDB ENTRY 1BNK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AN EQUIMOLAR RATIO OF DELTA79AAG AND REMARK 280 13-MER SINGLE-STRANDED (SS) EDC DNA WERE MIXED TO FORM A PROTEIN- REMARK 280 DNA COMPLEX CONCENTRATION OF 0.3 MM IN THE COMPLEX BUFFER (20 MM REMARK 280 HEPES-NAOH, PH 7.5, 100 MM NACL, 0.1 MM EDTA, 5% V/V GLYCEROL AND REMARK 280 1 MM DTT). THE COMPLEX WAS INCUBATED ON ICE FOR 15 MIN AND USED REMARK 280 FOR CRYSTALLIZATION. CRYSTALS WERE OBTAINED UPON MIXING 1 UL OF REMARK 280 PROTEIN-DNA COMPLEX AND 1 UL OF RESERVOIR SOLUTION (100 MM BIS- REMARK 280 TRIS, PH 5.5, 200 MM CESIUM CHLORIDE AND 20% POLYETHYLENE GLYCOL REMARK 280 (PEG) 3350) OVER 0.5 ML OF RESERVOIR SOLUTION. CRYSTALS APPEARED REMARK 280 AFTER INCUBATION FOR 14 DAYS AT 22 DEGREES C, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 131.27300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 196.90950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.63650 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 0.000000 1.000000 0.000000 41.16800 REMARK 350 BIOMT2 1 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 65.63650 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ARG A 201 REMARK 465 LYS A 202 REMARK 465 GLY A 203 REMARK 465 THR A 204 REMARK 465 ALA A 205 REMARK 465 SER A 206 REMARK 465 ARG A 207 REMARK 465 VAL A 208 REMARK 465 GLY A 265 REMARK 465 HIS A 266 REMARK 465 GLN A 294 REMARK 465 ASP A 295 REMARK 465 THR A 296 REMARK 465 GLN A 297 REMARK 465 ALA A 298 REMARK 465 GLU B 131 REMARK 465 ASP B 132 REMARK 465 GLU B 133 REMARK 465 ALA B 134 REMARK 465 ALA B 135 REMARK 465 HIS B 136 REMARK 465 SER B 137 REMARK 465 ARG B 138 REMARK 465 GLY B 139 REMARK 465 GLY B 140 REMARK 465 ARG B 141 REMARK 465 THR B 199 REMARK 465 LEU B 200 REMARK 465 ARG B 201 REMARK 465 LYS B 202 REMARK 465 GLY B 203 REMARK 465 THR B 204 REMARK 465 ALA B 205 REMARK 465 SER B 206 REMARK 465 GLU B 253 REMARK 465 PRO B 254 REMARK 465 GLY B 263 REMARK 465 VAL B 264 REMARK 465 GLY B 265 REMARK 465 HIS B 266 REMARK 465 ALA B 267 REMARK 465 GLY B 268 REMARK 465 GLU B 269 REMARK 465 TRP B 270 REMARK 465 ALA B 271 REMARK 465 ARG B 272 REMARK 465 LYS B 273 REMARK 465 ARG B 290 REMARK 465 VAL B 291 REMARK 465 ALA B 292 REMARK 465 GLU B 293 REMARK 465 GLN B 294 REMARK 465 ASP B 295 REMARK 465 THR B 296 REMARK 465 GLN B 297 REMARK 465 ALA B 298 REMARK 465 DC C 12 REMARK 465 DT C 13 REMARK 465 DT D 9 REMARK 465 DG D 10 REMARK 465 DC D 11 REMARK 465 DC D 12 REMARK 465 DT D 13 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 LEU A 200 CG CD1 CD2 REMARK 470 LEU A 209 CG CD1 CD2 REMARK 470 GLU A 250 CG CD OE1 OE2 REMARK 470 PRO B 144 CG CD REMARK 470 ILE B 161 CG1 CG2 CD1 REMARK 470 MET B 164 CG SD CE REMARK 470 ARG B 212 CG CD NE CZ NH1 NH2 REMARK 470 DG C 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DG C 1 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG C 1 C2 N2 N3 C4 REMARK 470 DC C 11 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC C 11 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC C 11 C6 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 PRO B 144 N - CA - CB ANGL. DEV. = 7.3 DEGREES REMARK 500 DG D 1 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT D 8 O4' - C1' - N1 ANGL. DEV. = 3.0 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 THR B 84 -166.78 -114.84 REMARK 500 PRO B 251 158.08 -48.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QI5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALKYLADENINE DNA GLYCOSYLASE IN REMARK 900 COMPLEX WITH 3,N4-ETHENOCYSTOSINE CONTAINING DUPLEX DNA REMARK 900 RELATED ID: 1EWN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE REMARK 900 COMPLEXED WITH 1,N6-ETHENOADENINE-DNA REMARK 900 RELATED ID: 1F4R RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE REMARK 900 COMPLEXED WITH 1,N6-ETHENOADENINE-DNA REMARK 900 RELATED ID: 1F6O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE REMARK 900 COMPLEXED WITH DNA REMARK 900 RELATED ID: 1BNK RELATED DB: PDB REMARK 900 HUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA DBREF 3UBY A 84 298 UNP P29372 3MG_HUMAN 84 298 DBREF 3UBY B 84 298 UNP P29372 3MG_HUMAN 84 298 DBREF 3UBY C 1 13 PDB 3UBY 3UBY 1 13 DBREF 3UBY D 1 13 PDB 3UBY 3UBY 1 13 SEQADV 3UBY GLY A 80 UNP P29372 EXPRESSION TAG SEQADV 3UBY PRO A 81 UNP P29372 EXPRESSION TAG SEQADV 3UBY HIS A 82 UNP P29372 EXPRESSION TAG SEQADV 3UBY MET A 83 UNP P29372 EXPRESSION TAG SEQADV 3UBY GLY B 80 UNP P29372 EXPRESSION TAG SEQADV 3UBY PRO B 81 UNP P29372 EXPRESSION TAG SEQADV 3UBY HIS B 82 UNP P29372 EXPRESSION TAG SEQADV 3UBY MET B 83 UNP P29372 EXPRESSION TAG SEQRES 1 A 219 GLY PRO HIS MET THR ARG LEU GLY LEU GLU PHE PHE ASP SEQRES 2 A 219 GLN PRO ALA VAL PRO LEU ALA ARG ALA PHE LEU GLY GLN SEQRES 3 A 219 VAL LEU VAL ARG ARG LEU PRO ASN GLY THR GLU LEU ARG SEQRES 4 A 219 GLY ARG ILE VAL GLU THR GLU ALA TYR LEU GLY PRO GLU SEQRES 5 A 219 ASP GLU ALA ALA HIS SER ARG GLY GLY ARG GLN THR PRO SEQRES 6 A 219 ARG ASN ARG GLY MET PHE MET LYS PRO GLY THR LEU TYR SEQRES 7 A 219 VAL TYR ILE ILE TYR GLY MET TYR PHE CYS MET ASN ILE SEQRES 8 A 219 SER SER GLN GLY ASP GLY ALA CYS VAL LEU LEU ARG ALA SEQRES 9 A 219 LEU GLU PRO LEU GLU GLY LEU GLU THR MET ARG GLN LEU SEQRES 10 A 219 ARG SER THR LEU ARG LYS GLY THR ALA SER ARG VAL LEU SEQRES 11 A 219 LYS ASP ARG GLU LEU CYS SER GLY PRO SER LYS LEU CYS SEQRES 12 A 219 GLN ALA LEU ALA ILE ASN LYS SER PHE ASP GLN ARG ASP SEQRES 13 A 219 LEU ALA GLN ASP GLU ALA VAL TRP LEU GLU ARG GLY PRO SEQRES 14 A 219 LEU GLU PRO SER GLU PRO ALA VAL VAL ALA ALA ALA ARG SEQRES 15 A 219 VAL GLY VAL GLY HIS ALA GLY GLU TRP ALA ARG LYS PRO SEQRES 16 A 219 LEU ARG PHE TYR VAL ARG GLY SER PRO TRP VAL SER VAL SEQRES 17 A 219 VAL ASP ARG VAL ALA GLU GLN ASP THR GLN ALA SEQRES 1 B 219 GLY PRO HIS MET THR ARG LEU GLY LEU GLU PHE PHE ASP SEQRES 2 B 219 GLN PRO ALA VAL PRO LEU ALA ARG ALA PHE LEU GLY GLN SEQRES 3 B 219 VAL LEU VAL ARG ARG LEU PRO ASN GLY THR GLU LEU ARG SEQRES 4 B 219 GLY ARG ILE VAL GLU THR GLU ALA TYR LEU GLY PRO GLU SEQRES 5 B 219 ASP GLU ALA ALA HIS SER ARG GLY GLY ARG GLN THR PRO SEQRES 6 B 219 ARG ASN ARG GLY MET PHE MET LYS PRO GLY THR LEU TYR SEQRES 7 B 219 VAL TYR ILE ILE TYR GLY MET TYR PHE CYS MET ASN ILE SEQRES 8 B 219 SER SER GLN GLY ASP GLY ALA CYS VAL LEU LEU ARG ALA SEQRES 9 B 219 LEU GLU PRO LEU GLU GLY LEU GLU THR MET ARG GLN LEU SEQRES 10 B 219 ARG SER THR LEU ARG LYS GLY THR ALA SER ARG VAL LEU SEQRES 11 B 219 LYS ASP ARG GLU LEU CYS SER GLY PRO SER LYS LEU CYS SEQRES 12 B 219 GLN ALA LEU ALA ILE ASN LYS SER PHE ASP GLN ARG ASP SEQRES 13 B 219 LEU ALA GLN ASP GLU ALA VAL TRP LEU GLU ARG GLY PRO SEQRES 14 B 219 LEU GLU PRO SER GLU PRO ALA VAL VAL ALA ALA ALA ARG SEQRES 15 B 219 VAL GLY VAL GLY HIS ALA GLY GLU TRP ALA ARG LYS PRO SEQRES 16 B 219 LEU ARG PHE TYR VAL ARG GLY SER PRO TRP VAL SER VAL SEQRES 17 B 219 VAL ASP ARG VAL ALA GLU GLN ASP THR GLN ALA SEQRES 1 C 13 DG DA DC DA DT DG EDC DT DT DG DC DC DT SEQRES 1 D 13 DG DA DC DA DT DG EDC DT DT DG DC DC DT HET EDC C 7 21 HET EDC D 7 21 HETNAM EDC N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE HETSYN EDC 6-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETSYN 2 EDC PENTOFURANOSYL)IMIDAZO[1,2-C]PYRIMIDIN-5(6H)-ONE FORMUL 3 EDC 2(C11 H14 N3 O7 P) FORMUL 5 HOH *250(H2 O) HELIX 1 1 GLY A 87 ASP A 92 1 6 HELIX 2 2 PRO A 94 PHE A 102 1 9 HELIX 3 3 SER A 137 ARG A 141 5 5 HELIX 4 4 PRO A 144 MET A 151 5 8 HELIX 5 5 GLY A 189 LEU A 200 1 12 HELIX 6 6 LYS A 210 LEU A 214 5 5 HELIX 7 7 GLY A 217 LEU A 225 1 9 HELIX 8 8 ASN A 228 ASP A 232 5 5 HELIX 9 9 SER A 252 PRO A 254 5 3 HELIX 10 10 GLY B 87 ASP B 92 1 6 HELIX 11 11 PRO B 94 PHE B 102 1 9 HELIX 12 12 ASN B 146 MET B 151 5 6 HELIX 13 13 GLY B 189 SER B 198 1 10 HELIX 14 14 LYS B 210 LEU B 214 5 5 HELIX 15 15 GLY B 217 LEU B 225 1 9 HELIX 16 16 ASN B 228 ASP B 232 5 5 SHEET 1 A 6 LEU A 156 ILE A 161 0 SHEET 2 A 6 TYR A 165 SER A 171 -1 O TYR A 165 N ILE A 161 SHEET 3 A 6 CYS A 178 GLU A 188 -1 O LEU A 181 N MET A 168 SHEET 4 A 6 GLU A 116 TYR A 127 -1 N ARG A 120 O GLU A 185 SHEET 5 A 6 VAL A 106 ARG A 110 -1 N ARG A 109 O LEU A 117 SHEET 6 A 6 VAL A 242 GLU A 245 -1 O TRP A 243 N VAL A 108 SHEET 1 B 6 LEU A 156 ILE A 161 0 SHEET 2 B 6 TYR A 165 SER A 171 -1 O TYR A 165 N ILE A 161 SHEET 3 B 6 CYS A 178 GLU A 188 -1 O LEU A 181 N MET A 168 SHEET 4 B 6 GLU A 116 TYR A 127 -1 N ARG A 120 O GLU A 185 SHEET 5 B 6 ARG A 276 VAL A 279 -1 O PHE A 277 N THR A 124 SHEET 6 B 6 VAL A 256 ALA A 259 -1 N VAL A 257 O TYR A 278 SHEET 1 C 7 THR B 84 ARG B 85 0 SHEET 2 C 7 VAL B 242 ARG B 246 -1 O ARG B 246 N THR B 84 SHEET 3 C 7 VAL B 106 ARG B 110 -1 N VAL B 108 O TRP B 243 SHEET 4 C 7 GLU B 116 TYR B 127 -1 O GLY B 119 N LEU B 107 SHEET 5 C 7 CYS B 178 GLU B 188 -1 O LEU B 187 N ARG B 118 SHEET 6 C 7 TYR B 165 SER B 171 -1 N ILE B 170 O VAL B 179 SHEET 7 C 7 LEU B 156 ILE B 161 -1 N TYR B 157 O ASN B 169 SHEET 1 D 6 THR B 84 ARG B 85 0 SHEET 2 D 6 VAL B 242 ARG B 246 -1 O ARG B 246 N THR B 84 SHEET 3 D 6 VAL B 106 ARG B 110 -1 N VAL B 108 O TRP B 243 SHEET 4 D 6 GLU B 116 TYR B 127 -1 O GLY B 119 N LEU B 107 SHEET 5 D 6 ARG B 276 VAL B 279 -1 O PHE B 277 N THR B 124 SHEET 6 D 6 VAL B 256 ALA B 259 -1 N ALA B 259 O ARG B 276 LINK O3' DG C 6 P EDC C 7 1555 1555 1.59 LINK O3' EDC C 7 P DT C 8 1555 1555 1.60 LINK O3' DG D 6 P EDC D 7 1555 1555 1.61 LINK O3' EDC D 7 P DT D 8 1555 1555 1.60 CRYST1 41.168 41.168 262.546 90.00 90.00 90.00 P 43 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 0.024291 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003809 0.00000 MASTER 469 0 2 16 25 0 0 6 0 0 0 36 END