HEADER HYDROLASE 23-JUN-21 7OY7 TITLE CRYSTAL STRUCTURE OF A TRAPPED PAB-AGOG/DOUBLE-STANDED DNA COVALENT TITLE 2 INTERMEDIATE (DNA CONTAINING CYTOSINE OPPOSITE TO LESION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-GLYCOSYLASE/DNA LYASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 8-OXOGUANINE DNA GLYCOSYLASE,AGOG,DNA-(APURINIC OR COMPND 5 APYRIMIDINIC SITE) LYASE,AP LYASE; COMPND 6 EC: 3.2.2.-,4.2.99.18; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*AP*GP*AP*AP*AP*CP*AP*AP*A)-3'); COMPND 14 CHAIN: I; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI (STRAIN GE5 / ORSAY); SOURCE 3 ORGANISM_TAXID: 272844; SOURCE 4 STRAIN: GE5 / ORSAY; SOURCE 5 GENE: PYRAB10170, PAB1695; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS 8-OXOGUANINE DNA GLYCOSYLASE, PYROCOCCUS ABYSSI, TRAPPED DOUBLE- KEYWDS 2 STRANDED DNA INTERMEDIATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.COSTE,S.GOFFINONT,D.FLAMENT,B.CASTAING REVDAT 3 31-JAN-24 7OY7 1 REMARK REVDAT 2 11-JAN-23 7OY7 1 JRNL REVDAT 1 13-JUL-22 7OY7 0 JRNL AUTH C.FRANCK,G.STEPHANE,C.JULIEN,G.VIRGINIE,G.MARTINE,G.NORBERT, JRNL AUTH 2 C.FABRICE,F.DIDIER,S.M.JOSEF,C.BERTRAND JRNL TITL STRUCTURAL AND FUNCTIONAL DETERMINANTS OF THE ARCHAEAL JRNL TITL 2 8-OXOGUANINE-DNA GLYCOSYLASE AGOG FOR DNA DAMAGE RECOGNITION JRNL TITL 3 AND PROCESSING. JRNL REF NUCLEIC ACIDS RES. V. 50 11072 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 36300625 JRNL DOI 10.1093/NAR/GKAC932 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 33030 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.8700 - 3.8900 1.00 2762 145 0.1387 0.1546 REMARK 3 2 3.8900 - 3.0900 1.00 2670 141 0.1459 0.1718 REMARK 3 3 3.0900 - 2.7000 1.00 2640 138 0.1664 0.1870 REMARK 3 4 2.7000 - 2.4500 1.00 2621 138 0.1635 0.2540 REMARK 3 5 2.4500 - 2.2800 1.00 2627 138 0.1664 0.2072 REMARK 3 6 2.2800 - 2.1400 1.00 2571 134 0.1637 0.2094 REMARK 3 7 2.1400 - 2.0300 1.00 2600 137 0.1663 0.2519 REMARK 3 8 2.0300 - 1.9500 1.00 2587 135 0.1842 0.2604 REMARK 3 9 1.9500 - 1.8700 1.00 2579 136 0.2238 0.2926 REMARK 3 10 1.8700 - 1.8100 1.00 2572 144 0.2537 0.3226 REMARK 3 11 1.8100 - 1.7500 1.00 2576 149 0.2903 0.3217 REMARK 3 12 1.7500 - 1.7000 0.99 2568 122 0.3259 0.3816 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.94 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -2 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.7241 -26.3789 -28.5077 REMARK 3 T TENSOR REMARK 3 T11: 0.1915 T22: 0.2333 REMARK 3 T33: 0.2276 T12: -0.0092 REMARK 3 T13: 0.0146 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 1.1858 L22: 5.0372 REMARK 3 L33: 0.5677 L12: -0.3264 REMARK 3 L13: 0.2009 L23: -0.4685 REMARK 3 S TENSOR REMARK 3 S11: 0.0698 S12: 0.0450 S13: -0.1420 REMARK 3 S21: 0.0097 S22: -0.0659 S23: 0.1427 REMARK 3 S31: 0.0223 S32: -0.0488 S33: -0.0153 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 37 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.5429 -7.3879 -19.2062 REMARK 3 T TENSOR REMARK 3 T11: 0.2270 T22: 0.2029 REMARK 3 T33: 0.2306 T12: -0.0025 REMARK 3 T13: -0.0187 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 3.1659 L22: 1.6909 REMARK 3 L33: 3.2874 L12: -0.6109 REMARK 3 L13: -0.6576 L23: -1.2135 REMARK 3 S TENSOR REMARK 3 S11: 0.0142 S12: 0.0070 S13: 0.0979 REMARK 3 S21: 0.0511 S22: 0.0100 S23: -0.0471 REMARK 3 S31: -0.1591 S32: -0.0882 S33: -0.0360 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7264 -7.6322 -10.7316 REMARK 3 T TENSOR REMARK 3 T11: 0.2382 T22: 0.1956 REMARK 3 T33: 0.1799 T12: 0.0025 REMARK 3 T13: -0.0038 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 1.0967 L22: 2.2265 REMARK 3 L33: 2.7317 L12: -0.6907 REMARK 3 L13: -0.9709 L23: -0.4733 REMARK 3 S TENSOR REMARK 3 S11: 0.0765 S12: -0.2677 S13: 0.0811 REMARK 3 S21: 0.2283 S22: 0.0421 S23: 0.0247 REMARK 3 S31: -0.1634 S32: -0.2016 S33: -0.1040 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 112 THROUGH 174 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.7679 -19.5904 -17.5758 REMARK 3 T TENSOR REMARK 3 T11: 0.2058 T22: 0.2524 REMARK 3 T33: 0.2891 T12: -0.0188 REMARK 3 T13: -0.0251 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 0.5404 L22: 1.0547 REMARK 3 L33: 1.6371 L12: -0.1053 REMARK 3 L13: -0.0653 L23: 0.1914 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: -0.0776 S13: -0.0934 REMARK 3 S21: 0.0633 S22: 0.0025 S23: -0.1539 REMARK 3 S31: 0.0697 S32: 0.0785 S33: 0.0075 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 175 THROUGH 188 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.9641 -35.6376 -12.0327 REMARK 3 T TENSOR REMARK 3 T11: 0.2749 T22: 0.3056 REMARK 3 T33: 0.2650 T12: -0.0670 REMARK 3 T13: 0.0287 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 3.3450 L22: 6.5484 REMARK 3 L33: 3.9352 L12: 1.8997 REMARK 3 L13: 0.0717 L23: 0.0693 REMARK 3 S TENSOR REMARK 3 S11: 0.1290 S12: -0.2529 S13: -0.0931 REMARK 3 S21: -0.2714 S22: -0.0746 S23: 0.2303 REMARK 3 S31: 0.3400 S32: -0.1835 S33: -0.0788 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 189 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.9958 -33.7133 -18.7764 REMARK 3 T TENSOR REMARK 3 T11: 0.2218 T22: 0.2092 REMARK 3 T33: 0.2166 T12: -0.0401 REMARK 3 T13: -0.0118 T23: -0.0146 REMARK 3 L TENSOR REMARK 3 L11: 4.8612 L22: 4.3334 REMARK 3 L33: 4.6946 L12: 0.6637 REMARK 3 L13: -1.0860 L23: -1.0275 REMARK 3 S TENSOR REMARK 3 S11: 0.1730 S12: -0.2183 S13: -0.1431 REMARK 3 S21: 0.1082 S22: -0.1286 S23: -0.2162 REMARK 3 S31: 0.0175 S32: -0.0997 S33: -0.0445 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 216 THROUGH 239 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.2426 -36.3596 -32.0756 REMARK 3 T TENSOR REMARK 3 T11: 0.1983 T22: 0.1968 REMARK 3 T33: 0.2740 T12: -0.0305 REMARK 3 T13: -0.0302 T23: -0.0193 REMARK 3 L TENSOR REMARK 3 L11: 1.9013 L22: 2.9415 REMARK 3 L33: 9.3880 L12: 0.9444 REMARK 3 L13: 0.0679 L23: -2.0109 REMARK 3 S TENSOR REMARK 3 S11: 0.0238 S12: -0.0120 S13: -0.0649 REMARK 3 S21: -0.2147 S22: 0.1216 S23: 0.1615 REMARK 3 S31: 0.3866 S32: -0.1726 S33: -0.1511 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.9490 -18.5338 -2.8133 REMARK 3 T TENSOR REMARK 3 T11: 0.3343 T22: 0.3754 REMARK 3 T33: 0.3063 T12: 0.0658 REMARK 3 T13: 0.0423 T23: 0.0884 REMARK 3 L TENSOR REMARK 3 L11: 2.9910 L22: 5.1315 REMARK 3 L33: 5.0622 L12: -1.2910 REMARK 3 L13: -3.5560 L23: -0.4190 REMARK 3 S TENSOR REMARK 3 S11: -0.3085 S12: -0.2716 S13: -0.2307 REMARK 3 S21: 0.6940 S22: 0.4145 S23: 0.5673 REMARK 3 S31: -0.0896 S32: -0.1845 S33: -0.1826 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.2419 -15.7917 -0.0753 REMARK 3 T TENSOR REMARK 3 T11: 0.4409 T22: 0.4581 REMARK 3 T33: 0.4189 T12: 0.0050 REMARK 3 T13: 0.0086 T23: 0.0307 REMARK 3 L TENSOR REMARK 3 L11: 9.7788 L22: 6.1154 REMARK 3 L33: 5.9002 L12: -2.8305 REMARK 3 L13: 2.7915 L23: -3.0037 REMARK 3 S TENSOR REMARK 3 S11: -0.1404 S12: -0.7672 S13: -0.1713 REMARK 3 S21: 0.7956 S22: 0.5152 S23: 0.4286 REMARK 3 S31: -0.3024 S32: -0.8076 S33: -0.4565 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7OY7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292116607. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33127 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 46.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.97800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 7OUE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MGCL2, NA ACETATE PH 5.0, MPD, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.26750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.26750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.79950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.91600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.79950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.91600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.26750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.79950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.91600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.26750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.79950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.91600 REMARK 290 SMTRY3 8 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: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, I 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 515 LIES ON A SPECIAL POSITION. 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 LYS A 57 CD CE NZ REMARK 470 LYS A 75 CG CD CE NZ REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 ARG A 103 NE CZ NH1 NH2 REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 LYS A 183 CE NZ REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 LYS A 195 CE NZ REMARK 470 LYS A 230 CE NZ REMARK 470 GLU A 233 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 114 O HOH A 401 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 I 2 O3' DG I 2 C3' -0.044 REMARK 500 DA I 4 O3' DA I 4 C3' -0.045 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 PED B 4 O3' - P - O5' ANGL. DEV. = -15.9 DEGREES REMARK 500 PED B 4 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DT B 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC I 6 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA I 9 O3' - P - OP2 ANGL. DEV. = 7.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 55 49.56 -107.00 REMARK 500 LYS A 75 -92.58 -103.86 REMARK 500 ASP A 123 66.58 -152.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 7OY7 A 1 239 UNP Q9UZY0 AGOG_PYRAB 1 239 DBREF 7OY7 B 1 9 PDB 7OY7 7OY7 1 9 DBREF 7OY7 I 1 9 PDB 7OY7 7OY7 1 9 SEQADV 7OY7 GLY A -2 UNP Q9UZY0 EXPRESSION TAG SEQADV 7OY7 SER A -1 UNP Q9UZY0 EXPRESSION TAG SEQADV 7OY7 HIS A 0 UNP Q9UZY0 EXPRESSION TAG SEQRES 1 A 242 GLY SER HIS MET ILE ALA ARG ILE ILE GLY GLU ILE GLY SEQRES 2 A 242 ILE GLU GLY ALA ARG PHE ILE GLU GLU ASN ILE ASP GLU SEQRES 3 A 242 GLN PHE LYS ALA LEU ARG TYR LEU SER LYS GLY ILE ASP SEQRES 4 A 242 SER GLU THR PHE VAL LYS LEU VAL ILE ALA ASN SER LEU SEQRES 5 A 242 VAL SER TYR GLN LEU THR GLY LYS GLY GLU GLN TRP TRP SEQRES 6 A 242 TRP GLU PHE ALA LYS TYR PHE TYR GLY ARG ASP VAL LYS SEQRES 7 A 242 SER ILE TYR LEU ALA TYR LYS GLU PHE LEU PRO ASN SER SEQRES 8 A 242 ARG PHE ASN ARG ARG LEU ILE PRO GLN LYS LEU SER ARG SEQRES 9 A 242 ILE ARG ARG VAL GLU THR PHE LEU SER THR LEU THR GLU SEQRES 10 A 242 GLU ARG ILE GLU GLU TYR TYR GLY ASP MET SER SER LEU SEQRES 11 A 242 TRP GLY SER ILE ALA ARG ALA LEU GLY VAL ASP LYS GLU SEQRES 12 A 242 SER LYS THR VAL VAL PHE SER VAL LYS MET PHE GLY TYR SEQRES 13 A 242 ALA ALA ARG ILE VAL LEU SER THR PHE ASN PRO TYR PRO SEQRES 14 A 242 MET GLU ILE PRO ILE PRO GLU ASP SER ARG ILE VAL LYS SEQRES 15 A 242 LEU THR LYS LYS LEU THR ASN GLU LYS PRO ARG LYS PHE SEQRES 16 A 242 TRP MET LYS ILE ALA ARG GLU SER GLY VAL PRO PRO LEU SEQRES 17 A 242 HIS ILE ASP SER ILE LEU TRP PRO LEU LEU GLY GLY ALA SEQRES 18 A 242 SER ILE ASP SER ALA PRO PRO GLU LEU ARG ASP LYS LEU SEQRES 19 A 242 ALA GLU LEU ILE LYS ILE ILE ARG SEQRES 1 B 9 DT DT DT PED DT DT DT DC DT SEQRES 1 I 9 DA DG DA DA DA DC DA DA DA HET PED B 4 11 HET MPD A 301 8 HETNAM PED PENTANE-3,4-DIOL-5-PHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN PED OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE FORMUL 2 PED C5 H13 O6 P FORMUL 4 MPD C6 H14 O2 FORMUL 5 HOH *280(H2 O) HELIX 1 AA1 GLY A -2 ILE A 21 1 24 HELIX 2 AA2 ASP A 22 LYS A 33 1 12 HELIX 3 AA3 ASP A 36 VAL A 50 1 15 HELIX 4 AA4 LYS A 57 TYR A 70 1 14 HELIX 5 AA5 SER A 76 LEU A 85 1 10 HELIX 6 AA6 PRO A 86 SER A 88 5 3 HELIX 7 AA7 LEU A 94 SER A 110 1 17 HELIX 8 AA8 THR A 113 GLY A 122 1 10 HELIX 9 AA9 ASP A 123 GLY A 136 1 14 HELIX 10 AB1 SER A 141 SER A 160 1 20 HELIX 11 AB2 ASP A 174 THR A 185 1 12 HELIX 12 AB3 LYS A 188 GLY A 201 1 14 HELIX 13 AB4 PRO A 203 GLY A 216 1 14 HELIX 14 AB5 PRO A 224 ARG A 239 1 16 LINK NZ LYS A 142 C1' PED B 4 1555 1555 1.44 LINK O3' DT B 3 P PED B 4 1555 1555 1.56 LINK O3' PED B 4 P DT B 5 1555 1555 1.56 CRYST1 59.599 71.832 138.535 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016779 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013921 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007218 0.00000