HEADER LYASE/DNA 18-MAR-09 3GO8 TITLE MUTM ENCOUNTERING AN INTRAHELICAL 8-OXOGUANINE (OXOG) LESION IN EC3- TITLE 2 LOOP DELETION COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MUTM; COMPND 5 SYNONYM: FAPY-DNA GLYCOSYLASE,DNA-(APURINIC OR APYRIMIDINIC SITE) COMPND 6 LYASE MUTM,AP LYASE MUTM; COMPND 7 EC: 3.2.2.23,4.2.99.18; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 5'-D(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*G)-3'; COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-D(*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*C)-3'; COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_COMMON: BACILLUS STEAROTHERMOPHILUS; SOURCE 4 ORGANISM_TAXID: 1422; SOURCE 5 GENE: MUTM, FPG; 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 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: SYNTHETIC DNA; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 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 M.C.SPONG,Y.QI,G.L.VERDINE REVDAT 7 06-SEP-23 3GO8 1 REMARK REVDAT 6 20-OCT-21 3GO8 1 REMARK SEQADV LINK REVDAT 5 06-FEB-19 3GO8 1 COMPND SOURCE DBREF SEQADV REVDAT 5 2 1 HET HETNAM FORMUL REVDAT 4 01-NOV-17 3GO8 1 REMARK REVDAT 3 13-JUL-11 3GO8 1 VERSN REVDAT 2 29-DEC-09 3GO8 1 JRNL REVDAT 1 15-DEC-09 3GO8 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. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 34033 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1685 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) : 1.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2156 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.1820 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1963 REMARK 3 NUCLEIC ACID ATOMS : 575 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 244 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) : 28.86 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): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 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 : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2673 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3740 ; 1.347 ; 2.251 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 254 ; 5.453 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 88 ;25.731 ;21.023 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 344 ;13.905 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;15.886 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1843 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1080 ; 0.191 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1748 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 253 ; 0.120 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.140 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.171 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 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 : 10 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 33 REMARK 3 ORIGIN FOR THE GROUP (A): 21.4720 -12.8030 9.7660 REMARK 3 T TENSOR REMARK 3 T11: -0.0475 T22: -0.0187 REMARK 3 T33: -0.0393 T12: -0.0213 REMARK 3 T13: -0.0189 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 1.0944 L22: 1.2347 REMARK 3 L33: 0.9798 L12: 0.1733 REMARK 3 L13: -0.2352 L23: 0.3237 REMARK 3 S TENSOR REMARK 3 S11: 0.0095 S12: -0.1070 S13: 0.0286 REMARK 3 S21: 0.0335 S22: -0.0239 S23: -0.1542 REMARK 3 S31: -0.0051 S32: 0.1186 S33: 0.0143 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 34 A 73 REMARK 3 ORIGIN FOR THE GROUP (A): 13.5040 -14.9440 5.0710 REMARK 3 T TENSOR REMARK 3 T11: -0.0134 T22: -0.0131 REMARK 3 T33: -0.0263 T12: 0.0106 REMARK 3 T13: -0.0219 T23: -0.0159 REMARK 3 L TENSOR REMARK 3 L11: 0.7861 L22: 1.0605 REMARK 3 L33: 0.5021 L12: 0.2450 REMARK 3 L13: -0.2546 L23: 0.4884 REMARK 3 S TENSOR REMARK 3 S11: 0.0360 S12: 0.0039 S13: -0.0139 REMARK 3 S21: -0.0337 S22: -0.0775 S23: -0.0105 REMARK 3 S31: -0.0569 S32: -0.0851 S33: 0.0415 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 108 REMARK 3 ORIGIN FOR THE GROUP (A): 25.1310 -18.2290 12.6980 REMARK 3 T TENSOR REMARK 3 T11: -0.0247 T22: 0.0376 REMARK 3 T33: -0.0322 T12: 0.0159 REMARK 3 T13: 0.0049 T23: -0.0282 REMARK 3 L TENSOR REMARK 3 L11: 1.0865 L22: 0.2352 REMARK 3 L33: 0.4005 L12: -0.3505 REMARK 3 L13: -0.6519 L23: 0.2250 REMARK 3 S TENSOR REMARK 3 S11: -0.0049 S12: -0.1499 S13: 0.0384 REMARK 3 S21: 0.0222 S22: 0.0390 S23: -0.0504 REMARK 3 S31: 0.0245 S32: 0.0666 S33: -0.0341 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 109 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): 13.4140 -15.6230 13.6780 REMARK 3 T TENSOR REMARK 3 T11: 0.0159 T22: 0.0056 REMARK 3 T33: -0.0553 T12: 0.0037 REMARK 3 T13: 0.0114 T23: -0.0252 REMARK 3 L TENSOR REMARK 3 L11: 0.9611 L22: 0.1170 REMARK 3 L33: 2.7762 L12: -0.0487 REMARK 3 L13: 0.9987 L23: 0.3955 REMARK 3 S TENSOR REMARK 3 S11: -0.0282 S12: -0.0258 S13: 0.0323 REMARK 3 S21: 0.0283 S22: 0.0228 S23: 0.1437 REMARK 3 S31: 0.0850 S32: 0.0508 S33: 0.0054 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 124 A 133 REMARK 3 ORIGIN FOR THE GROUP (A): 2.8220 -9.1720 6.8290 REMARK 3 T TENSOR REMARK 3 T11: -0.0514 T22: 0.0199 REMARK 3 T33: -0.0170 T12: 0.0455 REMARK 3 T13: -0.0344 T23: -0.1051 REMARK 3 L TENSOR REMARK 3 L11: 4.9283 L22: 4.9086 REMARK 3 L33: 10.1226 L12: -0.4287 REMARK 3 L13: 1.5463 L23: 5.4758 REMARK 3 S TENSOR REMARK 3 S11: 0.3073 S12: 0.1211 S13: 0.2195 REMARK 3 S21: -0.0101 S22: -0.6868 S23: 0.3521 REMARK 3 S31: 0.2548 S32: -0.5456 S33: 0.3795 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 134 A 200 REMARK 3 ORIGIN FOR THE GROUP (A): 4.9090 7.8890 22.8080 REMARK 3 T TENSOR REMARK 3 T11: -0.0197 T22: -0.0362 REMARK 3 T33: -0.0115 T12: 0.0406 REMARK 3 T13: -0.0209 T23: -0.0717 REMARK 3 L TENSOR REMARK 3 L11: 0.5685 L22: 1.0254 REMARK 3 L33: 1.7457 L12: 0.0921 REMARK 3 L13: -0.1468 L23: 0.8863 REMARK 3 S TENSOR REMARK 3 S11: 0.0793 S12: 0.0390 S13: -0.0071 REMARK 3 S21: -0.0343 S22: -0.1545 S23: 0.0916 REMARK 3 S31: -0.0272 S32: -0.0459 S33: 0.0752 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 201 A 216 REMARK 3 ORIGIN FOR THE GROUP (A): 14.1800 12.2770 20.0080 REMARK 3 T TENSOR REMARK 3 T11: 0.0326 T22: -0.0645 REMARK 3 T33: -0.0127 T12: 0.0044 REMARK 3 T13: 0.0338 T23: -0.0182 REMARK 3 L TENSOR REMARK 3 L11: 11.3615 L22: 6.1564 REMARK 3 L33: 1.2015 L12: -6.4383 REMARK 3 L13: -2.9856 L23: 2.7144 REMARK 3 S TENSOR REMARK 3 S11: 0.1014 S12: 0.1252 S13: 0.3498 REMARK 3 S21: -0.4219 S22: -0.0706 S23: -0.3251 REMARK 3 S31: -0.2573 S32: 0.0225 S33: -0.0308 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 238 A 251 REMARK 3 ORIGIN FOR THE GROUP (A): 20.0870 8.1750 35.1250 REMARK 3 T TENSOR REMARK 3 T11: -0.0005 T22: -0.0097 REMARK 3 T33: -0.0475 T12: 0.0277 REMARK 3 T13: -0.0198 T23: -0.0504 REMARK 3 L TENSOR REMARK 3 L11: 2.2654 L22: 2.9007 REMARK 3 L33: 3.8708 L12: 2.1530 REMARK 3 L13: 0.3013 L23: 0.4595 REMARK 3 S TENSOR REMARK 3 S11: -0.0739 S12: 0.1511 S13: -0.0248 REMARK 3 S21: 0.0356 S22: 0.2340 S23: -0.2423 REMARK 3 S31: 0.2092 S32: 0.4609 S33: -0.1601 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 252 A 274 REMARK 3 ORIGIN FOR THE GROUP (A): 11.1160 7.4930 37.5370 REMARK 3 T TENSOR REMARK 3 T11: 0.0288 T22: -0.0308 REMARK 3 T33: -0.0385 T12: -0.0465 REMARK 3 T13: 0.0167 T23: -0.0558 REMARK 3 L TENSOR REMARK 3 L11: 1.6118 L22: 2.0583 REMARK 3 L33: 2.9893 L12: 1.3006 REMARK 3 L13: 1.9976 L23: 2.3317 REMARK 3 S TENSOR REMARK 3 S11: -0.0133 S12: -0.0123 S13: 0.0924 REMARK 3 S21: 0.2936 S22: -0.0633 S23: 0.1527 REMARK 3 S31: 0.2632 S32: -0.0031 S33: 0.0765 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 15 REMARK 3 RESIDUE RANGE : C 2 C 15 REMARK 3 ORIGIN FOR THE GROUP (A): 5.6020 -13.5390 30.3160 REMARK 3 T TENSOR REMARK 3 T11: 0.0337 T22: 0.0380 REMARK 3 T33: -0.0402 T12: 0.0549 REMARK 3 T13: 0.0857 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 4.0861 L22: 2.5822 REMARK 3 L33: 0.0025 L12: -0.9168 REMARK 3 L13: 0.0845 L23: -0.0619 REMARK 3 S TENSOR REMARK 3 S11: -0.2477 S12: -0.5239 S13: -0.1004 REMARK 3 S21: 0.4911 S22: 0.2986 S23: 0.5418 REMARK 3 S31: -0.0531 S32: 0.1705 S33: -0.0509 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 3GO8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052107. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-06 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 : 19-ID 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 QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35790 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8970 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 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: 2F5O PROTEIN PART ONLY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8K, SODIUM CACODYLATE, GLYCEROL, REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 22.62200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.62300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.32750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.62300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.62200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.32750 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: 4020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 233 REMARK 465 GLY A 234 REMARK 465 GLY A 235 REMARK 465 ASN A 236 REMARK 465 HIS A 237 REMARK 465 DA B 1 REMARK 465 DC B 16 REMARK 465 DT C 1 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 ARG A 80 CD NE CZ NH1 NH2 REMARK 470 GLU A 150 CD OE1 OE2 REMARK 470 LYS A 154 CG CD CE NZ REMARK 470 LYS A 156 CD CE NZ REMARK 470 MET A 216 CG SD CE REMARK 470 HIS A 238 CG ND1 CD2 CE1 NE2 REMARK 470 DG C 2 P OP1 OP2 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. = 2.0 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC C 15 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 66 -158.45 -108.80 REMARK 500 ARG A 76 -139.31 46.01 REMARK 500 ASP A 110 102.48 -166.66 REMARK 500 GLU A 133 -8.30 83.58 REMARK 500 VAL A 241 -32.62 -134.21 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 112.9 REMARK 620 3 CYS A 269 SG 115.0 101.9 REMARK 620 4 CYS A 272 SG 130.1 92.3 99.5 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: 3GQY 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 3GO8 A 2 274 UNP P84131 P84131_GEOSE 2 274 DBREF 3GO8 B 1 16 PDB 3GO8 3GO8 1 16 DBREF 3GO8 C 1 16 PDB 3GO8 3GO8 1 16 SEQADV 3GO8 GLU A 3 UNP P84131 GLN 3 CONFLICT SEQADV 3GO8 CYS A 166 UNP P84131 GLN 166 ENGINEERED MUTATION SEQADV 3GO8 A UNP P84131 SER 220 DELETION SEQADV 3GO8 A UNP P84131 THR 221 DELETION SEQADV 3GO8 A UNP P84131 VAL 222 DELETION SEQADV 3GO8 A UNP P84131 ARG 223 DELETION SEQADV 3GO8 A UNP P84131 THR 224 DELETION SEQADV 3GO8 A UNP P84131 TYR 225 DELETION SEQADV 3GO8 A UNP P84131 VAL 226 DELETION SEQADV 3GO8 A UNP P84131 THR 228 DELETION SEQADV 3GO8 A UNP P84131 GLN 229 DELETION SEQADV 3GO8 A UNP P84131 GLY 230 DELETION SEQADV 3GO8 A UNP P84131 GLU 231 DELETION SEQADV 3GO8 A UNP P84131 ALA 232 DELETION SEQADV 3GO8 A UNP P84131 GLY 233 DELETION SEQADV 3GO8 A UNP P84131 THR 234 DELETION SEQADV 3GO8 A UNP P84131 PHE 235 DELETION SEQADV 3GO8 A UNP P84131 GLN 236 DELETION SEQRES 1 A 257 PRO GLU LEU PRO GLU VAL GLU THR ILE ARG ARG THR LEU SEQRES 2 A 257 LEU PRO LEU ILE VAL GLY LYS THR ILE GLU ASP VAL ARG SEQRES 3 A 257 ILE PHE TRP PRO ASN ILE ILE ARG HIS PRO ARG ASP SER SEQRES 4 A 257 GLU ALA PHE ALA ALA ARG MET ILE GLY GLN THR VAL ARG SEQRES 5 A 257 GLY LEU GLU ARG ARG GLY LYS PHE LEU LYS PHE LEU LEU SEQRES 6 A 257 ASP ARG ASP ALA LEU ILE SER HIS LEU ARG MET GLU GLY SEQRES 7 A 257 ARG TYR ALA VAL ALA SER ALA LEU GLU PRO LEU GLU PRO SEQRES 8 A 257 HIS THR HIS VAL VAL PHE CYS PHE THR ASP GLY SER GLU SEQRES 9 A 257 LEU ARG TYR ARG ASP VAL ARG LYS PHE GLY THR MET HIS SEQRES 10 A 257 VAL TYR ALA LYS GLU GLU ALA ASP ARG ARG PRO PRO LEU SEQRES 11 A 257 ALA GLU LEU GLY PRO GLU PRO LEU SER PRO ALA PHE SER SEQRES 12 A 257 PRO ALA VAL LEU ALA GLU ARG ALA VAL LYS THR LYS ARG SEQRES 13 A 257 SER VAL LYS ALA LEU LEU LEU ASP CYS THR VAL VAL ALA SEQRES 14 A 257 GLY PHE GLY ASN ILE TYR VAL ASP GLU SER LEU PHE ARG SEQRES 15 A 257 ALA GLY ILE LEU PRO GLY ARG PRO ALA ALA SER LEU SER SEQRES 16 A 257 SER LYS GLU ILE GLU ARG LEU HIS GLU GLU MET VAL ALA SEQRES 17 A 257 THR ILE GLY GLU ALA VAL MET LYS GLY GLY ASN HIS HIS SEQRES 18 A 257 LEU TYR VAL TYR GLY ARG GLN GLY ASN PRO CYS LYS ARG SEQRES 19 A 257 CYS GLY THR PRO ILE GLU LYS THR VAL VAL ALA GLY ARG SEQRES 20 A 257 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 3GO8 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 *244(H2 O) HELIX 1 2 TRP A 30 ASN A 32 5 3 HELIX 2 3 ASP A 39 ILE A 48 1 10 HELIX 3 4 GLU A 123 ARG A 128 5 6 HELIX 4 5 SER A 144 LYS A 154 1 11 HELIX 5 6 SER A 158 LEU A 164 1 7 HELIX 6 7 GLY A 173 GLY A 185 1 13 HELIX 7 8 PRO A 191 LEU A 195 5 5 HELIX 8 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 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 2.27 LINK SG CYS A 252 ZN ZN A 300 1555 1555 2.31 LINK SG CYS A 269 ZN ZN A 300 1555 1555 2.30 LINK SG CYS A 272 ZN ZN A 300 1555 1555 2.68 CISPEP 1 HIS A 36 PRO A 37 0 -9.46 CISPEP 2 PRO A 129 PRO A 130 0 1.59 SITE 1 AC1 4 CYS A 249 CYS A 252 CYS A 269 CYS A 272 CRYST1 45.244 92.655 105.246 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 0.022102 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009502 0.00000