HEADER LYASE/DNA 23-MAR-09 3GPY TITLE SEQUENCE-MATCHED MUTM LESION RECOGNITION COMPLEX 3 (LRC3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.2.99.18; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*C)- COMPND 9 3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*T*GP*CP*GP*TP*CP*CP*(8OG) COMPND 14 P*GP*AP*TP*CP*TP*AP*CP*C)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_COMMON: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 4 ORGANISM_TAXID: 1422; SOURCE 5 GENE: MUTM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC DNA; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: SYNTHETIC DNA KEYWDS DNA GLYCOSYLASE, DNA REPAIR, DAMAGE SEARCH, BASE EXTRUSION, DISULFIDE KEYWDS 2 CROSSLINKING, DNA DAMAGE, DNA-BINDING, GLYCOSIDASE, HYDROLASE, KEYWDS 3 LYASE, METAL-BINDING, MULTIFUNCTIONAL ENZYME, ZINC-FINGER, LYASE-DNA KEYWDS 4 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.QI,G.L.VERDINE REVDAT 6 06-SEP-23 3GPY 1 REMARK REVDAT 5 20-OCT-21 3GPY 1 REMARK SEQADV LINK REVDAT 4 01-NOV-17 3GPY 1 REMARK REVDAT 3 13-JUL-11 3GPY 1 VERSN REVDAT 2 02-FEB-10 3GPY 1 JRNL REVDAT 1 10-NOV-09 3GPY 0 JRNL AUTH Y.QI,M.C.SPONG,K.NAM,A.BANERJEE,S.JIRALERSPONG,M.KARPLUS, JRNL AUTH 2 G.L.VERDINE JRNL TITL ENCOUNTER AND EXTRUSION OF AN INTRAHELICAL LESION BY A DNA JRNL TITL 2 REPAIR ENZYME. JRNL REF NATURE V. 462 762 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 20010681 JRNL DOI 10.1038/NATURE08561 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0066 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 36463 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1820 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2280 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.1760 REMARK 3 BIN FREE R VALUE SET COUNT : 123 REMARK 3 BIN FREE R VALUE : 0.2220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2127 REMARK 3 NUCLEIC ACID ATOMS : 631 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 297 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2902 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4063 ; 1.391 ; 2.246 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 5.255 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 97 ;26.819 ;21.443 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 369 ;11.737 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;16.803 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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): 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 : 7 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): -17.6970 63.3750 9.6410 REMARK 3 T TENSOR REMARK 3 T11: 0.0170 T22: 0.0143 REMARK 3 T33: -0.0446 T12: 0.0049 REMARK 3 T13: 0.0003 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.2301 L22: 0.3074 REMARK 3 L33: 0.7310 L12: -0.1238 REMARK 3 L13: 0.1268 L23: -0.2615 REMARK 3 S TENSOR REMARK 3 S11: -0.0074 S12: -0.0314 S13: -0.0083 REMARK 3 S21: -0.0180 S22: 0.0045 S23: -0.0066 REMARK 3 S31: -0.0063 S32: -0.0110 S33: 0.0029 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 124 A 133 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6200 57.4070 7.0920 REMARK 3 T TENSOR REMARK 3 T11: -0.0462 T22: 0.0546 REMARK 3 T33: -0.0622 T12: 0.0257 REMARK 3 T13: 0.0233 T23: 0.0849 REMARK 3 L TENSOR REMARK 3 L11: 7.3195 L22: 12.1860 REMARK 3 L33: 10.2720 L12: -3.1873 REMARK 3 L13: -1.4422 L23: -6.4886 REMARK 3 S TENSOR REMARK 3 S11: 0.0980 S12: 0.0336 S13: -0.1612 REMARK 3 S21: 0.0130 S22: -0.6101 S23: -0.6473 REMARK 3 S31: -0.1451 S32: 0.5035 S33: 0.5121 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 : A 134 A 200 REMARK 3 ORIGIN FOR THE GROUP (A): -4.3650 40.0740 22.4360 REMARK 3 T TENSOR REMARK 3 T11: 0.0003 T22: 0.0226 REMARK 3 T33: -0.0124 T12: 0.0470 REMARK 3 T13: 0.0442 T23: 0.0695 REMARK 3 L TENSOR REMARK 3 L11: 0.2238 L22: 0.4126 REMARK 3 L33: 1.2189 L12: -0.0654 REMARK 3 L13: -0.1306 L23: -0.3583 REMARK 3 S TENSOR REMARK 3 S11: 0.0226 S12: -0.0308 S13: 0.0118 REMARK 3 S21: -0.1206 S22: -0.1664 S23: -0.0726 REMARK 3 S31: 0.1356 S32: 0.1015 S33: 0.1438 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 : A 201 A 215 REMARK 3 ORIGIN FOR THE GROUP (A): -12.5440 35.3740 18.8730 REMARK 3 T TENSOR REMARK 3 T11: 0.1082 T22: -0.0467 REMARK 3 T33: -0.0690 T12: 0.0200 REMARK 3 T13: 0.0552 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 12.7056 L22: 3.7993 REMARK 3 L33: 1.9811 L12: -4.8066 REMARK 3 L13: 3.9439 L23: -2.6706 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: 0.1162 S13: -0.3202 REMARK 3 S21: -0.4617 S22: -0.0432 S23: 0.0153 REMARK 3 S31: 0.3816 S32: -0.0287 S33: 0.0487 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 216 A 240 REMARK 3 ORIGIN FOR THE GROUP (A): -25.4670 46.7750 21.3560 REMARK 3 T TENSOR REMARK 3 T11: -0.0365 T22: 0.0502 REMARK 3 T33: -0.0239 T12: -0.0162 REMARK 3 T13: -0.0065 T23: 0.0469 REMARK 3 L TENSOR REMARK 3 L11: 0.1741 L22: 3.2787 REMARK 3 L33: 2.9624 L12: -0.7228 REMARK 3 L13: 0.5832 L23: -1.8912 REMARK 3 S TENSOR REMARK 3 S11: 0.0940 S12: -0.1162 S13: -0.1131 REMARK 3 S21: -0.0743 S22: 0.2111 S23: 0.1439 REMARK 3 S31: 0.0643 S32: -0.3981 S33: -0.3050 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 241 A 274 REMARK 3 ORIGIN FOR THE GROUP (A): -14.9930 39.8470 36.0730 REMARK 3 T TENSOR REMARK 3 T11: 0.0224 T22: -0.0021 REMARK 3 T33: -0.0361 T12: -0.0197 REMARK 3 T13: -0.0080 T23: 0.0325 REMARK 3 L TENSOR REMARK 3 L11: 0.7546 L22: 2.4361 REMARK 3 L33: 0.8512 L12: 0.3546 REMARK 3 L13: -0.6490 L23: -1.1205 REMARK 3 S TENSOR REMARK 3 S11: 0.0758 S12: -0.0291 S13: -0.0031 REMARK 3 S21: 0.1082 S22: -0.1115 S23: -0.0302 REMARK 3 S31: -0.0450 S32: 0.0239 S33: 0.0358 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 16 REMARK 3 RESIDUE RANGE : C 1 C 15 REMARK 3 ORIGIN FOR THE GROUP (A): -8.1500 59.1440 33.8390 REMARK 3 T TENSOR REMARK 3 T11: 0.0751 T22: 0.0122 REMARK 3 T33: -0.0613 T12: 0.0117 REMARK 3 T13: -0.0167 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 1.6372 L22: 1.5379 REMARK 3 L33: 1.2824 L12: -1.2176 REMARK 3 L13: 1.3524 L23: -1.3291 REMARK 3 S TENSOR REMARK 3 S11: -0.2278 S12: -0.0137 S13: 0.0321 REMARK 3 S21: 0.4077 S22: 0.1274 S23: -0.1685 REMARK 3 S31: -0.2549 S32: -0.0767 S33: 0.1004 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 3GPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052167. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37987 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1790 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.63100 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: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1R2Y, PROTEIN PART ONLY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8K, SODIUM CACODYLATE, GLYCEROL, REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 22.45200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.11900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.60350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.11900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.45200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.60350 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: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 DT C 1 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 GLU A 88 CD OE1 OE2 REMARK 470 LYS A 154 CE NZ REMARK 470 LYS A 156 CE NZ REMARK 470 LYS A 198 CD CE NZ REMARK 470 ARG A 251 CD NE CZ NH1 NH2 REMARK 470 ARG A 274 CG CD NE CZ NH1 NH2 REMARK 470 DG C 2 P OP1 OP2 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 DG C 2 C6 DG C 2 N1 -0.052 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 DG B 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 8 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG C 2 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DC C 7 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA C 10 O4' - C1' - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 DC C 16 O4' - C1' - N1 ANGL. DEV. = 2.8 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 GLN A 3 -169.01 -109.88 REMARK 500 LEU A 66 -140.94 -104.66 REMARK 500 ARG A 76 -120.19 47.95 REMARK 500 ASP A 110 95.51 -162.63 REMARK 500 ARG A 223 -64.91 -142.17 REMARK 500 VAL A 241 -40.21 -130.27 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 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 249 SG REMARK 620 2 CYS A 252 SG 109.7 REMARK 620 3 CYS A 269 SG 111.3 98.4 REMARK 620 4 CYS A 272 SG 108.9 111.0 117.1 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 ZN A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GPP RELATED DB: PDB REMARK 900 RELATED ID: 3GPU RELATED DB: PDB REMARK 900 RELATED ID: 3GPX RELATED DB: PDB REMARK 900 RELATED ID: 3GQ3 RELATED DB: PDB REMARK 900 RELATED ID: 3GQ4 RELATED DB: PDB REMARK 900 RELATED ID: 3GQ5 RELATED DB: PDB DBREF 3GPY A 2 274 UNP P84131 P84131_BACST 2 274 DBREF 3GPY B 1 16 PDB 3GPY 3GPY 1 16 DBREF 3GPY C 1 16 PDB 3GPY 3GPY 1 16 SEQADV 3GPY CYS A 166 UNP P84131 GLN 166 ENGINEERED MUTATION SEQRES 1 A 273 PRO GLN LEU PRO GLU VAL GLU THR ILE ARG ARG THR LEU SEQRES 2 A 273 LEU PRO LEU ILE VAL GLY LYS THR ILE GLU ASP VAL ARG SEQRES 3 A 273 ILE PHE TRP PRO ASN ILE ILE ARG HIS PRO ARG ASP SER SEQRES 4 A 273 GLU ALA PHE ALA ALA ARG MET ILE GLY GLN THR VAL ARG SEQRES 5 A 273 GLY LEU GLU ARG ARG GLY LYS PHE LEU LYS PHE LEU LEU SEQRES 6 A 273 ASP ARG ASP ALA LEU ILE SER HIS LEU ARG MET GLU GLY SEQRES 7 A 273 ARG TYR ALA VAL ALA SER ALA LEU GLU PRO LEU GLU PRO SEQRES 8 A 273 HIS THR HIS VAL VAL PHE CYS PHE THR ASP GLY SER GLU SEQRES 9 A 273 LEU ARG TYR ARG ASP VAL ARG LYS PHE GLY THR MET HIS SEQRES 10 A 273 VAL TYR ALA LYS GLU GLU ALA ASP ARG ARG PRO PRO LEU SEQRES 11 A 273 ALA GLU LEU GLY PRO GLU PRO LEU SER PRO ALA PHE SER SEQRES 12 A 273 PRO ALA VAL LEU ALA GLU ARG ALA VAL LYS THR LYS ARG SEQRES 13 A 273 SER VAL LYS ALA LEU LEU LEU ASP CYS THR VAL VAL ALA SEQRES 14 A 273 GLY PHE GLY ASN ILE TYR VAL ASP GLU SER LEU PHE ARG SEQRES 15 A 273 ALA GLY ILE LEU PRO GLY ARG PRO ALA ALA SER LEU SER SEQRES 16 A 273 SER LYS GLU ILE GLU ARG LEU HIS GLU GLU MET VAL ALA SEQRES 17 A 273 THR ILE GLY GLU ALA VAL MET LYS GLY GLY SER THR VAL SEQRES 18 A 273 ARG THR TYR VAL ASN THR GLN GLY GLU ALA GLY THR PHE SEQRES 19 A 273 GLN HIS HIS LEU TYR VAL TYR GLY ARG GLN GLY ASN PRO SEQRES 20 A 273 CYS LYS ARG CYS GLY THR PRO ILE GLU LYS THR VAL VAL SEQRES 21 A 273 ALA GLY ARG GLY THR HIS TYR CYS PRO ARG CYS GLN ARG SEQRES 1 B 16 DA DG DG DT DA DG DA DT DC DC DG DG DA SEQRES 2 B 16 DC DG DC SEQRES 1 C 16 DT DG DC DG DT DC DC 8OG DG DA DT DC DT SEQRES 2 C 16 DA DC DC MODRES 3GPY 8OG C 8 DG HET 8OG C 8 23 HET ZN A 300 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 3 8OG C10 H14 N5 O8 P FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *297(H2 O) HELIX 1 1 GLN A 3 VAL A 19 1 17 HELIX 2 2 TRP A 30 ASN A 32 5 3 HELIX 3 3 ASP A 39 ILE A 48 1 10 HELIX 4 4 GLU A 124 ARG A 128 5 5 HELIX 5 5 SER A 144 VAL A 153 1 10 HELIX 6 6 SER A 158 ASP A 165 1 8 HELIX 7 7 GLY A 173 GLY A 185 1 13 HELIX 8 8 PRO A 191 LEU A 195 5 5 HELIX 9 9 SER A 196 LYS A 217 1 22 HELIX 10 10 THR A 234 LEU A 239 5 6 SHEET 1 A 4 ILE A 23 ILE A 28 0 SHEET 2 A 4 THR A 94 PHE A 100 -1 O CYS A 99 N GLU A 24 SHEET 3 A 4 SER A 104 ARG A 109 -1 O TYR A 108 N VAL A 96 SHEET 4 A 4 ARG A 80 SER A 85 -1 N ALA A 82 O ARG A 107 SHEET 1 B 5 ILE A 34 HIS A 36 0 SHEET 2 B 5 THR A 116 ALA A 121 1 O MET A 117 N ARG A 35 SHEET 3 B 5 ASP A 69 HIS A 74 -1 N ILE A 72 O HIS A 118 SHEET 4 B 5 PHE A 61 LEU A 65 -1 N PHE A 64 O LEU A 71 SHEET 5 B 5 GLY A 54 ARG A 58 -1 N GLU A 56 O LYS A 63 SHEET 1 C 2 GLU A 257 VAL A 261 0 SHEET 2 C 2 ARG A 264 TYR A 268 -1 O TYR A 268 N GLU A 257 LINK O3' DC C 7 P 8OG C 8 1555 1555 1.60 LINK O3' 8OG C 8 P DG C 9 1555 1555 1.60 LINK SG CYS A 249 ZN ZN A 300 1555 1555 2.36 LINK SG CYS A 252 ZN ZN A 300 1555 1555 2.34 LINK SG CYS A 269 ZN ZN A 300 1555 1555 2.29 LINK SG CYS A 272 ZN ZN A 300 1555 1555 2.33 CISPEP 1 HIS A 36 PRO A 37 0 -11.87 CISPEP 2 PRO A 129 PRO A 130 0 5.45 SITE 1 AC1 4 CYS A 249 CYS A 252 CYS A 269 CYS A 272 CRYST1 44.904 95.207 102.238 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 0.022270 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009781 0.00000