PDB Short entry for 3GPU HEADER LYASE/DNA 23-MAR-09 3GPU TITLE MUTM ENCOUNTERING AN INTRAHELICAL 8-OXOGUANINE (OXOG) LESION IN EC4- TITLE 2 LOOP DELETION COMPLEX 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*CP*TP*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(*TP*GP*CP*GP*TP*CP*CP*(8OG) COMPND 14 P*AP*GP*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 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES 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 A.BANERJEE,Y.QI,G.L.VERDINE REVDAT 6 06-SEP-23 3GPU 1 REMARK REVDAT 5 20-OCT-21 3GPU 1 REMARK SEQADV LINK REVDAT 4 01-NOV-17 3GPU 1 REMARK REVDAT 3 13-JUL-11 3GPU 1 VERSN REVDAT 2 02-FEB-10 3GPU 1 JRNL REVDAT 1 10-NOV-09 3GPU 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. 1.62 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) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 54101 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2748 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) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3477 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 198 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1962 REMARK 3 NUCLEIC ACID ATOMS : 515 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 287 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) : 26.28 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): 0.083 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.079 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 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 : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2616 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3649 ; 1.333 ; 2.228 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 255 ; 5.537 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;25.783 ;20.778 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 348 ;12.568 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;15.593 ;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 : 8 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 34 REMARK 3 ORIGIN FOR THE GROUP (A): 21.1480 -13.1430 9.7770 REMARK 3 T TENSOR REMARK 3 T11: -0.0342 T22: -0.0117 REMARK 3 T33: -0.0632 T12: -0.0077 REMARK 3 T13: -0.0093 T23: -0.0092 REMARK 3 L TENSOR REMARK 3 L11: 0.9814 L22: 1.3719 REMARK 3 L33: 1.4358 L12: 0.0526 REMARK 3 L13: -0.3654 L23: 0.4497 REMARK 3 S TENSOR REMARK 3 S11: 0.0109 S12: -0.1104 S13: 0.0482 REMARK 3 S21: 0.0064 S22: -0.0056 S23: -0.0966 REMARK 3 S31: -0.0362 S32: 0.0987 S33: -0.0053 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 35 A 73 REMARK 3 ORIGIN FOR THE GROUP (A): 13.4630 -14.9000 4.8810 REMARK 3 T TENSOR REMARK 3 T11: -0.0047 T22: -0.0072 REMARK 3 T33: -0.0455 T12: 0.0093 REMARK 3 T13: -0.0071 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 0.7293 L22: 1.3968 REMARK 3 L33: 0.8181 L12: 0.0446 REMARK 3 L13: -0.1060 L23: 0.6520 REMARK 3 S TENSOR REMARK 3 S11: 0.0455 S12: 0.0034 S13: 0.0233 REMARK 3 S21: -0.0338 S22: -0.0673 S23: 0.0280 REMARK 3 S31: -0.0455 S32: -0.0900 S33: 0.0217 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 74 A 110 REMARK 3 ORIGIN FOR THE GROUP (A): 24.9450 -18.1160 13.0910 REMARK 3 T TENSOR REMARK 3 T11: 0.0207 T22: 0.0194 REMARK 3 T33: -0.0630 T12: 0.0060 REMARK 3 T13: 0.0082 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 1.0365 L22: 0.7304 REMARK 3 L33: 0.5519 L12: -0.4988 REMARK 3 L13: -0.5095 L23: 0.3581 REMARK 3 S TENSOR REMARK 3 S11: -0.0088 S12: -0.1456 S13: 0.0366 REMARK 3 S21: 0.0982 S22: 0.0346 S23: -0.0514 REMARK 3 S31: 0.0245 S32: 0.1050 S33: -0.0257 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 111 A 154 REMARK 3 ORIGIN FOR THE GROUP (A): 5.9330 -3.7300 12.2630 REMARK 3 T TENSOR REMARK 3 T11: -0.0062 T22: 0.0249 REMARK 3 T33: -0.0321 T12: 0.0203 REMARK 3 T13: -0.0195 T23: -0.0525 REMARK 3 L TENSOR REMARK 3 L11: 0.0215 L22: 1.0890 REMARK 3 L33: 1.4708 L12: 0.0477 REMARK 3 L13: 0.0502 L23: 1.2650 REMARK 3 S TENSOR REMARK 3 S11: 0.0105 S12: -0.0115 S13: 0.0099 REMARK 3 S21: -0.2021 S22: -0.2200 S23: 0.1423 REMARK 3 S31: -0.0634 S32: -0.2026 S33: 0.2095 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 155 A 199 REMARK 3 ORIGIN FOR THE GROUP (A): 5.8630 7.5780 26.1520 REMARK 3 T TENSOR REMARK 3 T11: -0.0095 T22: -0.0259 REMARK 3 T33: -0.0359 T12: 0.0107 REMARK 3 T13: -0.0036 T23: -0.0760 REMARK 3 L TENSOR REMARK 3 L11: 0.7644 L22: 1.3973 REMARK 3 L33: 2.5503 L12: -0.1166 REMARK 3 L13: 0.0491 L23: 1.3101 REMARK 3 S TENSOR REMARK 3 S11: 0.0734 S12: 0.0593 S13: 0.0048 REMARK 3 S21: 0.0500 S22: -0.1857 S23: 0.1109 REMARK 3 S31: 0.0765 S32: -0.1091 S33: 0.1123 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 200 A 216 REMARK 3 ORIGIN FOR THE GROUP (A): 13.2360 12.5370 19.8210 REMARK 3 T TENSOR REMARK 3 T11: 0.0535 T22: -0.0563 REMARK 3 T33: -0.0682 T12: 0.0075 REMARK 3 T13: 0.0226 T23: -0.0133 REMARK 3 L TENSOR REMARK 3 L11: 13.5251 L22: 6.9700 REMARK 3 L33: 2.6540 L12: -6.5155 REMARK 3 L13: -2.6734 L23: 2.8665 REMARK 3 S TENSOR REMARK 3 S11: 0.3041 S12: 0.1770 S13: 0.3453 REMARK 3 S21: -0.5178 S22: -0.2252 S23: -0.3681 REMARK 3 S31: -0.4260 S32: 0.0927 S33: -0.0790 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 239 A 274 REMARK 3 ORIGIN FOR THE GROUP (A): 14.7500 7.9610 36.5280 REMARK 3 T TENSOR REMARK 3 T11: 0.0408 T22: -0.0345 REMARK 3 T33: -0.0686 T12: -0.0051 REMARK 3 T13: -0.0033 T23: -0.0398 REMARK 3 L TENSOR REMARK 3 L11: 1.2207 L22: 3.0331 REMARK 3 L33: 2.4658 L12: 1.3744 REMARK 3 L13: 1.2092 L23: 2.2732 REMARK 3 S TENSOR REMARK 3 S11: 0.1210 S12: 0.0084 S13: -0.0008 REMARK 3 S21: 0.2908 S22: -0.0685 S23: -0.0155 REMARK 3 S31: 0.2417 S32: 0.0422 S33: -0.0525 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 14 REMARK 3 RESIDUE RANGE : C 4 C 15 REMARK 3 ORIGIN FOR THE GROUP (A): 3.7230 -12.5440 28.1820 REMARK 3 T TENSOR REMARK 3 T11: 0.0487 T22: -0.0086 REMARK 3 T33: -0.0238 T12: 0.0057 REMARK 3 T13: 0.0735 T23: -0.0411 REMARK 3 L TENSOR REMARK 3 L11: 3.2968 L22: 2.2407 REMARK 3 L33: 0.7723 L12: -0.3157 REMARK 3 L13: -0.0102 L23: -0.3515 REMARK 3 S TENSOR REMARK 3 S11: -0.1248 S12: -0.3171 S13: 0.0224 REMARK 3 S21: 0.3512 S22: 0.1172 S23: 0.5210 REMARK 3 S31: 0.0165 S32: -0.0718 S33: 0.0076 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 3GPU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-AUG-05 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 : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 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 : 56204 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.8820 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.49500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 2F5O, PROTEIN PART ONLY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 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 22.60900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.48600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.64700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.48600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.60900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.64700 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: 3730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 LYS A 234 REMARK 465 GLY A 235 REMARK 465 GLN A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 DA B 1 REMARK 465 DG B 15 REMARK 465 DC B 16 REMARK 465 DT C 1 REMARK 465 DG C 2 REMARK 465 DC C 3 REMARK 465 DC C 16 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 ARG A 38 CD NE CZ NH1 NH2 REMARK 470 GLU A 150 CG CD OE1 OE2 REMARK 470 LYS A 154 CD CE NZ REMARK 470 LYS A 156 CG CD CE NZ REMARK 470 MET A 216 CG SD CE 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 DT B 9 O4' - C1' - C2' ANGL. DEV. = 3.4 DEGREES REMARK 500 DG C 10 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA C 14 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC C 15 O4' - C1' - N1 ANGL. DEV. = 3.8 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 LEU A 66 -159.85 -108.63 REMARK 500 ARG A 76 -139.62 49.94 REMARK 500 ASP A 110 117.02 -164.13 REMARK 500 GLU A 133 -4.82 79.99 REMARK 500 VAL A 241 -35.31 -134.37 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 109.9 REMARK 620 3 CYS A 269 SG 110.9 98.3 REMARK 620 4 CYS A 272 SG 109.3 111.6 116.4 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: 3GPX RELATED DB: PDB REMARK 900 RELATED ID: 3GPY 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 3GPU A 2 274 UNP P84131 P84131_BACST 2 274 DBREF 3GPU B 1 16 PDB 3GPU 3GPU 1 16 DBREF 3GPU C 1 16 PDB 3GPU 3GPU 1 16 SEQADV 3GPU GLU A 3 UNP P84131 GLN 3 CONFLICT SEQADV 3GPU CYS A 166 UNP P84131 GLN 166 ENGINEERED MUTATION SEQADV 3GPU A UNP P84131 GLY 219 DELETION SEQADV 3GPU A UNP P84131 SER 220 DELETION SEQADV 3GPU A UNP P84131 THR 221 DELETION SEQADV 3GPU A UNP P84131 VAL 222 DELETION SEQADV 3GPU A UNP P84131 ARG 223 DELETION SEQADV 3GPU A UNP P84131 THR 224 DELETION SEQADV 3GPU A UNP P84131 TYR 225 DELETION SEQADV 3GPU A UNP P84131 VAL 226 DELETION SEQADV 3GPU A UNP P84131 ASN 227 DELETION SEQADV 3GPU A UNP P84131 THR 228 DELETION SEQADV 3GPU A UNP P84131 GLN 229 DELETION SEQADV 3GPU A UNP P84131 GLY 230 DELETION SEQADV 3GPU A UNP P84131 GLU 231 DELETION SEQADV 3GPU A UNP P84131 ALA 232 DELETION SEQADV 3GPU A UNP P84131 GLY 233 DELETION SEQADV 3GPU A UNP P84131 THR 234 DELETION SEQADV 3GPU A UNP P84131 PHE 235 DELETION SEQRES 1 A 256 PRO GLU LEU PRO GLU VAL GLU THR ILE ARG ARG THR LEU SEQRES 2 A 256 LEU PRO LEU ILE VAL GLY LYS THR ILE GLU ASP VAL ARG SEQRES 3 A 256 ILE PHE TRP PRO ASN ILE ILE ARG HIS PRO ARG ASP SER SEQRES 4 A 256 GLU ALA PHE ALA ALA ARG MET ILE GLY GLN THR VAL ARG SEQRES 5 A 256 GLY LEU GLU ARG ARG GLY LYS PHE LEU LYS PHE LEU LEU SEQRES 6 A 256 ASP ARG ASP ALA LEU ILE SER HIS LEU ARG MET GLU GLY SEQRES 7 A 256 ARG TYR ALA VAL ALA SER ALA LEU GLU PRO LEU GLU PRO SEQRES 8 A 256 HIS THR HIS VAL VAL PHE CYS PHE THR ASP GLY SER GLU SEQRES 9 A 256 LEU ARG TYR ARG ASP VAL ARG LYS PHE GLY THR MET HIS SEQRES 10 A 256 VAL TYR ALA LYS GLU GLU ALA ASP ARG ARG PRO PRO LEU SEQRES 11 A 256 ALA GLU LEU GLY PRO GLU PRO LEU SER PRO ALA PHE SER SEQRES 12 A 256 PRO ALA VAL LEU ALA GLU ARG ALA VAL LYS THR LYS ARG SEQRES 13 A 256 SER VAL LYS ALA LEU LEU LEU ASP CYS THR VAL VAL ALA SEQRES 14 A 256 GLY PHE GLY ASN ILE TYR VAL ASP GLU SER LEU PHE ARG SEQRES 15 A 256 ALA GLY ILE LEU PRO GLY ARG PRO ALA ALA SER LEU SER SEQRES 16 A 256 SER LYS GLU ILE GLU ARG LEU HIS GLU GLU MET VAL ALA SEQRES 17 A 256 THR ILE GLY GLU ALA VAL MET LYS GLY GLN HIS HIS LEU SEQRES 18 A 256 TYR VAL TYR GLY ARG GLN GLY ASN PRO CYS LYS ARG CYS SEQRES 19 A 256 GLY THR PRO ILE GLU LYS THR VAL VAL ALA GLY ARG GLY SEQRES 20 A 256 THR HIS TYR CYS PRO ARG CYS GLN ARG SEQRES 1 B 16 DA DG DG DT DA DG DA DC DT DC DG DG DA SEQRES 2 B 16 DC DG DC SEQRES 1 C 16 DT DG DC DG DT DC DC 8OG DA DG DT DC DT SEQRES 2 C 16 DA DC DC MODRES 3GPU 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 *287(H2 O) HELIX 1 1 GLU 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 123 ARG A 128 5 6 HELIX 5 5 SER A 144 LYS A 154 1 11 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 MET A 216 1 21 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 SER A 104 N PHE A 100 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 DA C 9 1555 1555 1.60 LINK SG CYS A 249 ZN ZN A 300 1555 1555 2.34 LINK SG CYS A 252 ZN ZN A 300 1555 1555 2.33 LINK SG CYS A 269 ZN ZN A 300 1555 1555 2.33 LINK SG CYS A 272 ZN ZN A 300 1555 1555 2.33 CISPEP 1 HIS A 36 PRO A 37 0 -12.46 CISPEP 2 PRO A 129 PRO A 130 0 3.43 SITE 1 AC1 4 CYS A 249 CYS A 252 CYS A 269 CYS A 272 CRYST1 45.218 93.294 104.972 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 0.022115 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009526 0.00000