HEADER HYDROLASE/DNA 20-MAR-09 3GP1 TITLE MUTM ENCOUNTERING AN INTRAHELICAL 8-OXOGUANINE (OXOG) LESION IN EC3- TITLE 2 V222P 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: 5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*CP**C)- COMPND 9 3'; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(P*TP*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*CP*C)- COMPND 14 3'; COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: MUTM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC DNA; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 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, KEYWDS 4 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.C.SPONG,Y.QI,G.L.VERDINE REVDAT 6 06-SEP-23 3GP1 1 REMARK REVDAT 5 20-OCT-21 3GP1 1 REMARK SEQADV LINK REVDAT 4 01-NOV-17 3GP1 1 REMARK REVDAT 3 13-JUL-11 3GP1 1 VERSN REVDAT 2 02-FEB-10 3GP1 1 JRNL REVDAT 1 10-NOV-09 3GP1 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. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 27498 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 : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1336 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1545 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1970 REMARK 3 NUCLEIC ACID ATOMS : 533 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 180 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) : 32.96 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): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 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 : 0.947 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): 2622 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3660 ; 1.482 ; 2.236 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 252 ; 5.490 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 88 ;26.536 ;21.136 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 344 ;13.863 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;15.134 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 409 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1814 ; 0.007 ; 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): 1265 ; 0.697 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2044 ; 1.301 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1357 ; 2.058 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1616 ; 3.196 ; 4.500 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 23 REMARK 3 ORIGIN FOR THE GROUP (A): 23.4470 -6.2770 8.5100 REMARK 3 T TENSOR REMARK 3 T11: -0.0217 T22: -0.0286 REMARK 3 T33: 0.0143 T12: -0.0467 REMARK 3 T13: -0.0001 T23: -0.0252 REMARK 3 L TENSOR REMARK 3 L11: 0.9761 L22: 3.4174 REMARK 3 L33: 3.1862 L12: -1.1445 REMARK 3 L13: -0.6965 L23: 2.5192 REMARK 3 S TENSOR REMARK 3 S11: -0.0001 S12: -0.0434 S13: 0.1619 REMARK 3 S21: -0.0480 S22: -0.0040 S23: -0.1548 REMARK 3 S31: -0.1353 S32: 0.1557 S33: 0.0041 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 24 A 48 REMARK 3 ORIGIN FOR THE GROUP (A): 14.1640 -24.0400 9.0190 REMARK 3 T TENSOR REMARK 3 T11: -0.0188 T22: 0.0123 REMARK 3 T33: -0.0028 T12: -0.0081 REMARK 3 T13: 0.0041 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.6316 L22: 2.0465 REMARK 3 L33: 0.0171 L12: 0.7108 REMARK 3 L13: -0.0855 L23: -0.1790 REMARK 3 S TENSOR REMARK 3 S11: 0.0719 S12: -0.0626 S13: -0.1618 REMARK 3 S21: 0.0606 S22: -0.1534 S23: 0.0460 REMARK 3 S31: 0.0968 S32: 0.0201 S33: 0.0815 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 49 A 73 REMARK 3 ORIGIN FOR THE GROUP (A): 15.2410 -10.1720 3.9360 REMARK 3 T TENSOR REMARK 3 T11: 0.0165 T22: -0.0158 REMARK 3 T33: -0.0061 T12: 0.0138 REMARK 3 T13: -0.0080 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 1.1632 L22: 1.5362 REMARK 3 L33: 1.3186 L12: -0.3585 REMARK 3 L13: -0.8104 L23: 1.1761 REMARK 3 S TENSOR REMARK 3 S11: 0.0210 S12: 0.0343 S13: 0.0739 REMARK 3 S21: -0.0981 S22: -0.0817 S23: 0.0081 REMARK 3 S31: -0.1121 S32: -0.0846 S33: 0.0608 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 74 A 112 REMARK 3 ORIGIN FOR THE GROUP (A): 24.9210 -17.9100 13.8320 REMARK 3 T TENSOR REMARK 3 T11: -0.0087 T22: 0.0351 REMARK 3 T33: -0.0206 T12: 0.0143 REMARK 3 T13: 0.0049 T23: -0.0248 REMARK 3 L TENSOR REMARK 3 L11: 1.0607 L22: 0.5869 REMARK 3 L33: 0.7756 L12: -0.4518 REMARK 3 L13: -0.8164 L23: 0.1068 REMARK 3 S TENSOR REMARK 3 S11: -0.0562 S12: -0.1094 S13: 0.0883 REMARK 3 S21: 0.0517 S22: 0.0664 S23: -0.0577 REMARK 3 S31: 0.0692 S32: 0.1060 S33: -0.0102 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 113 A 133 REMARK 3 ORIGIN FOR THE GROUP (A): 6.9030 -12.3940 8.3510 REMARK 3 T TENSOR REMARK 3 T11: -0.0479 T22: 0.0266 REMARK 3 T33: 0.0069 T12: -0.0150 REMARK 3 T13: 0.0010 T23: -0.0432 REMARK 3 L TENSOR REMARK 3 L11: 0.7521 L22: 1.7285 REMARK 3 L33: 2.7794 L12: -0.3807 REMARK 3 L13: 1.0973 L23: 0.7899 REMARK 3 S TENSOR REMARK 3 S11: 0.0588 S12: -0.0904 S13: 0.1463 REMARK 3 S21: -0.1155 S22: -0.2178 S23: 0.0970 REMARK 3 S31: 0.1465 S32: -0.1415 S33: 0.1589 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 198 REMARK 3 ORIGIN FOR THE GROUP (A): 5.0750 7.5790 22.5710 REMARK 3 T TENSOR REMARK 3 T11: -0.0132 T22: -0.0223 REMARK 3 T33: 0.0058 T12: 0.0415 REMARK 3 T13: -0.0345 T23: -0.0875 REMARK 3 L TENSOR REMARK 3 L11: 0.2652 L22: 1.3534 REMARK 3 L33: 2.0866 L12: -0.1823 REMARK 3 L13: -0.2219 L23: 1.3577 REMARK 3 S TENSOR REMARK 3 S11: 0.0720 S12: 0.0615 S13: 0.0230 REMARK 3 S21: -0.0448 S22: -0.1926 S23: 0.0761 REMARK 3 S31: 0.0049 S32: -0.0829 S33: 0.1205 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 199 A 216 REMARK 3 ORIGIN FOR THE GROUP (A): 12.6570 12.8280 20.1420 REMARK 3 T TENSOR REMARK 3 T11: 0.0518 T22: -0.0533 REMARK 3 T33: -0.0471 T12: 0.0085 REMARK 3 T13: 0.0074 T23: -0.0344 REMARK 3 L TENSOR REMARK 3 L11: 11.6273 L22: 5.0190 REMARK 3 L33: 4.3396 L12: -5.3438 REMARK 3 L13: -5.3196 L23: 4.6549 REMARK 3 S TENSOR REMARK 3 S11: 0.2569 S12: -0.2485 S13: 0.2309 REMARK 3 S21: -0.4538 S22: -0.0366 S23: -0.2186 REMARK 3 S31: -0.4339 S32: 0.1418 S33: -0.2203 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 250 REMARK 3 ORIGIN FOR THE GROUP (A): 20.6500 7.2240 34.7830 REMARK 3 T TENSOR REMARK 3 T11: -0.0041 T22: -0.0035 REMARK 3 T33: -0.0166 T12: 0.0646 REMARK 3 T13: 0.0132 T23: -0.0860 REMARK 3 L TENSOR REMARK 3 L11: 2.6480 L22: 10.0548 REMARK 3 L33: 10.9451 L12: 3.5890 REMARK 3 L13: 2.6000 L23: -3.0760 REMARK 3 S TENSOR REMARK 3 S11: -0.0188 S12: 0.2296 S13: -0.1664 REMARK 3 S21: -0.2667 S22: 0.2285 S23: -0.6151 REMARK 3 S31: 0.5813 S32: 0.7377 S33: -0.2097 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 251 A 274 REMARK 3 ORIGIN FOR THE GROUP (A): 11.7690 8.1800 37.0470 REMARK 3 T TENSOR REMARK 3 T11: 0.0396 T22: -0.0207 REMARK 3 T33: -0.0213 T12: -0.0401 REMARK 3 T13: 0.0333 T23: -0.0716 REMARK 3 L TENSOR REMARK 3 L11: 1.3585 L22: 2.7491 REMARK 3 L33: 1.5604 L12: 0.4863 REMARK 3 L13: 1.4386 L23: 0.8237 REMARK 3 S TENSOR REMARK 3 S11: 0.0822 S12: -0.0407 S13: 0.0719 REMARK 3 S21: 0.1768 S22: -0.1796 S23: 0.1221 REMARK 3 S31: 0.1896 S32: -0.1010 S33: 0.0974 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 1 B 14 REMARK 3 RESIDUE RANGE : C 3 C 15 REMARK 3 ORIGIN FOR THE GROUP (A): 4.1420 -12.7580 28.6060 REMARK 3 T TENSOR REMARK 3 T11: -0.0001 T22: -0.0089 REMARK 3 T33: 0.0207 T12: 0.0634 REMARK 3 T13: 0.0889 T23: 0.0282 REMARK 3 L TENSOR REMARK 3 L11: 5.7106 L22: 3.6049 REMARK 3 L33: 0.0968 L12: -1.7824 REMARK 3 L13: 0.4447 L23: 0.2966 REMARK 3 S TENSOR REMARK 3 S11: -0.5468 S12: -0.4527 S13: -0.1868 REMARK 3 S21: 0.4985 S22: 0.5249 S23: 0.7188 REMARK 3 S31: -0.0124 S32: 0.3136 S33: 0.0219 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 3GP1 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_1000052136. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-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) : 0.9790 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK HIGH-RESOLUTION REMARK 200 DOUBLE-CRYSTAL SI(111) REMARK 200 OPTICS : ROSENBAUM-ROCK VERTICAL FOCUSING REMARK 200 MIRROR, WITH PT, GLASS, PD REMARK 200 LANES. LN2 COOLED FIRST CRYSTAL, REMARK 200 SAGITTAL FOCUSING 2ND CRYSTAL 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 : 28412 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5880 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2F5O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, 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 22.80650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.50950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.42250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.50950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.80650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.42250 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: 2810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.1 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 217 REMARK 465 GLY A 218 REMARK 465 GLY A 219 REMARK 465 SER A 220 REMARK 465 THR A 221 REMARK 465 PRO A 222 REMARK 465 ARG A 223 REMARK 465 THR A 224 REMARK 465 TYR A 225 REMARK 465 VAL A 226 REMARK 465 ASN A 227 REMARK 465 THR A 228 REMARK 465 GLN A 229 REMARK 465 GLY A 230 REMARK 465 GLU A 231 REMARK 465 ALA A 232 REMARK 465 GLY A 233 REMARK 465 THR A 234 REMARK 465 PHE A 235 REMARK 465 GLN A 236 REMARK 465 HIS A 237 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 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 NE CZ NH1 NH2 REMARK 470 GLU A 150 CD OE1 OE2 REMARK 470 LYS A 154 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 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 DC B 14 C4 DC B 14 C5 0.057 REMARK 500 DG C 4 C6 DG C 4 N1 -0.045 REMARK 500 DG C 4 C5 DG C 4 N7 -0.042 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. = 2.5 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC B 14 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 DC B 14 C4 - C5 - C6 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG C 4 C4 - C5 - N7 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG C 4 C8 - N9 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG C 4 N9 - C4 - C5 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT C 11 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DC C 15 O4' - C1' - N1 ANGL. DEV. = 1.9 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 -158.63 -110.30 REMARK 500 ARG A 76 -139.60 51.51 REMARK 500 ASP A 110 106.46 -168.36 REMARK 500 GLU A 133 -6.98 79.98 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 109.1 REMARK 620 3 CYS A 269 SG 109.7 97.4 REMARK 620 4 CYS A 272 SG 111.3 108.5 119.7 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 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE SEQUENCE IN THE UNP DATABASE REMARK 999 IS NOT THE WILD-TYPE SEQUENCE, BUT HAS GLU 3 TO GLN 3 REMARK 999 MUTATION THAT MAKES THE ENZYME INACTIVE. THE SEQUENCE REMARK 999 WITH GLU AT POSITION 3 IS THE WILD-TYPE SEQUENCE. DBREF 3GP1 A 2 274 UNP P84131 P84131_BACST 2 274 DBREF 3GP1 B 1 16 PDB 3GP1 3GP1 1 16 DBREF 3GP1 C 1 15 PDB 3GP1 3GP1 1 15 SEQADV 3GP1 GLU A 3 UNP P84131 GLN 3 SEE REMARK 999 SEQADV 3GP1 CYS A 166 UNP P84131 GLN 166 ENGINEERED MUTATION SEQADV 3GP1 PRO A 222 UNP P84131 VAL 222 ENGINEERED MUTATION SEQRES 1 A 273 PRO GLU 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 PRO 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 15 DT DG DC DG DT DC DC 8OG DG DA DT DC DT SEQRES 2 C 15 DA DC MODRES 3GP1 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 *180(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 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 1.59 LINK SG CYS A 249 ZN ZN A 300 1555 1555 2.30 LINK SG CYS A 252 ZN ZN A 300 1555 1555 2.34 LINK SG CYS A 269 ZN ZN A 300 1555 1555 2.28 LINK SG CYS A 272 ZN ZN A 300 1555 1555 2.27 CISPEP 1 HIS A 36 PRO A 37 0 -9.32 CISPEP 2 PRO A 129 PRO A 130 0 0.06 SITE 1 AC1 4 CYS A 249 CYS A 252 CYS A 269 CYS A 272 CRYST1 45.613 92.845 105.019 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 0.021924 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010771 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009522 0.00000