HEADER HYDROLASE 28-JUL-21 7P9Z TITLE CRYSTAL STRUCTURE OF A TRAPPED PAB-AGOG/DOUBLE-STANDED DNA COVALENT TITLE 2 INTERMEDIATE (DNA CONTAINING ADENINE 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)*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*AP*AP*AP*A)-3'); COMPND 14 CHAIN: I; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 3 ORGANISM_TAXID: 29292; SOURCE 4 GENE: PYRAB10170, PAB1695; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 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 7P9Z 1 REMARK REVDAT 2 11-JAN-23 7P9Z 1 JRNL REVDAT 1 10-AUG-22 7P9Z 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. 1.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 66042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 3294 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 45.9900 - 3.8200 0.88 2401 109 0.1554 0.1714 REMARK 3 2 3.8200 - 3.0300 0.99 2633 158 0.1461 0.1627 REMARK 3 3 3.0300 - 2.6500 1.00 2658 136 0.1751 0.1702 REMARK 3 4 2.6500 - 2.4100 1.00 2636 125 0.1731 0.1741 REMARK 3 5 2.4100 - 2.2400 1.00 2652 134 0.1649 0.1653 REMARK 3 6 2.2400 - 2.1000 1.00 2562 177 0.1749 0.1969 REMARK 3 7 2.1000 - 2.0000 1.00 2625 154 0.1817 0.1863 REMARK 3 8 2.0000 - 1.9100 1.00 2652 128 0.1871 0.2235 REMARK 3 9 1.9100 - 1.8400 1.00 2600 161 0.1889 0.1847 REMARK 3 10 1.8400 - 1.7700 1.00 2647 113 0.1945 0.1963 REMARK 3 11 1.7700 - 1.7200 1.00 2615 121 0.2012 0.2283 REMARK 3 12 1.7200 - 1.6700 1.00 2668 126 0.2001 0.2102 REMARK 3 13 1.6700 - 1.6300 1.00 2620 135 0.1937 0.2492 REMARK 3 14 1.6300 - 1.5900 1.00 2595 147 0.1902 0.2051 REMARK 3 15 1.5900 - 1.5500 1.00 2658 129 0.1957 0.2044 REMARK 3 16 1.5500 - 1.5200 1.00 2633 123 0.1921 0.2148 REMARK 3 17 1.5200 - 1.4900 1.00 2609 135 0.1993 0.2730 REMARK 3 18 1.4900 - 1.4600 1.00 2608 158 0.2012 0.2202 REMARK 3 19 1.4600 - 1.4300 1.00 2593 157 0.2082 0.2109 REMARK 3 20 1.4300 - 1.4100 1.00 2611 148 0.2157 0.2530 REMARK 3 21 1.4100 - 1.3900 1.00 2659 124 0.2320 0.2690 REMARK 3 22 1.3900 - 1.3600 1.00 2604 114 0.2403 0.2548 REMARK 3 23 1.3600 - 1.3400 1.00 2626 131 0.2466 0.2863 REMARK 3 24 1.3400 - 1.3300 1.00 2583 151 0.2605 0.2842 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.21 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 : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1956 17.8409 32.8583 REMARK 3 T TENSOR REMARK 3 T11: 0.2643 T22: 0.3671 REMARK 3 T33: 0.2406 T12: 0.0289 REMARK 3 T13: -0.0381 T23: -0.0464 REMARK 3 L TENSOR REMARK 3 L11: 6.1261 L22: 6.0248 REMARK 3 L33: 6.1046 L12: -0.9573 REMARK 3 L13: -0.8035 L23: -3.1334 REMARK 3 S TENSOR REMARK 3 S11: -0.2286 S12: -0.1453 S13: 0.2872 REMARK 3 S21: 0.4374 S22: 0.2389 S23: -0.4813 REMARK 3 S31: -0.1129 S32: 0.3240 S33: -0.0444 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.8168 15.4696 35.4256 REMARK 3 T TENSOR REMARK 3 T11: 0.2972 T22: 0.5836 REMARK 3 T33: 0.3640 T12: 0.0743 REMARK 3 T13: -0.0268 T23: 0.0595 REMARK 3 L TENSOR REMARK 3 L11: 6.9471 L22: 8.5158 REMARK 3 L33: 5.1732 L12: -3.1792 REMARK 3 L13: -4.0901 L23: 4.9549 REMARK 3 S TENSOR REMARK 3 S11: 0.1124 S12: 0.1555 S13: 0.6734 REMARK 3 S21: 0.2210 S22: 0.0495 S23: -0.3032 REMARK 3 S31: 0.2449 S32: 0.3219 S33: -0.1141 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -2 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.0251 26.7514 6.0175 REMARK 3 T TENSOR REMARK 3 T11: 0.1058 T22: 0.1371 REMARK 3 T33: 0.1399 T12: -0.0131 REMARK 3 T13: -0.0060 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 1.6478 L22: 5.9047 REMARK 3 L33: 1.4997 L12: -0.4918 REMARK 3 L13: -0.3793 L23: 0.7259 REMARK 3 S TENSOR REMARK 3 S11: 0.0955 S12: -0.1199 S13: 0.2279 REMARK 3 S21: 0.0012 S22: -0.1094 S23: -0.0533 REMARK 3 S31: -0.0902 S32: 0.0693 S33: 0.0075 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 37 THROUGH 159 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.4140 11.9902 17.8670 REMARK 3 T TENSOR REMARK 3 T11: 0.1625 T22: 0.1763 REMARK 3 T33: 0.1466 T12: -0.0277 REMARK 3 T13: 0.0097 T23: 0.0443 REMARK 3 L TENSOR REMARK 3 L11: 1.8374 L22: 1.1456 REMARK 3 L33: 2.5074 L12: -0.2531 REMARK 3 L13: -0.2090 L23: 0.2844 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: -0.3148 S13: -0.2012 REMARK 3 S21: 0.1194 S22: -0.0500 S23: -0.0029 REMARK 3 S31: 0.2606 S32: 0.0479 S33: 0.0352 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 160 THROUGH 239 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6880 34.0471 13.0919 REMARK 3 T TENSOR REMARK 3 T11: 0.1513 T22: 0.1627 REMARK 3 T33: 0.2048 T12: -0.0071 REMARK 3 T13: 0.0060 T23: -0.0409 REMARK 3 L TENSOR REMARK 3 L11: 1.3244 L22: 1.4821 REMARK 3 L33: 3.0513 L12: 0.9527 REMARK 3 L13: 0.0983 L23: 0.4150 REMARK 3 S TENSOR REMARK 3 S11: 0.1627 S12: -0.2522 S13: 0.1282 REMARK 3 S21: 0.0839 S22: -0.0903 S23: -0.0299 REMARK 3 S31: -0.1578 S32: 0.2736 S33: -0.0688 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 7P9Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292117321. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-21 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 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98011 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66075 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 68.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 7OY7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MGCL2, NA ACETATE PH 5.0, MPD, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 30.92400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.38750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.92400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.38750 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: 2900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 520 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 598 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 GLU A 59 CG CD OE1 OE2 REMARK 470 LYS A 75 CG CD CE NZ REMARK 470 LYS A 82 CE NZ REMARK 470 ARG A 103 NE CZ NH1 NH2 REMARK 470 ARG A 133 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 179 CG CD CE NZ REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 LYS A 188 CD CE NZ REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 195 CG CD CE NZ 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 OE1 GLU A 114 O HOH A 401 2.17 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 I 2 O4' - C1' - N9 ANGL. DEV. = 3.0 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 50.49 -110.39 REMARK 500 LYS A 75 -90.10 -106.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 658 DISTANCE = 5.94 ANGSTROMS DBREF 7P9Z A 1 239 UNP Q9UZY0 AGOG_PYRAB 1 239 DBREF 7P9Z B 1 9 PDB 7P9Z 7P9Z 1 9 DBREF 7P9Z I 1 9 PDB 7P9Z 7P9Z 1 9 SEQADV 7P9Z GLY A -2 UNP Q9UZY0 EXPRESSION TAG SEQADV 7P9Z SER A -1 UNP Q9UZY0 EXPRESSION TAG SEQADV 7P9Z 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 DA 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 *317(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 ASP A 123 1 11 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 1.47 LINK O3' DT B 3 P PED B 4 1555 1555 1.59 LINK O3' PED B 4 P DT B 5 1555 1555 1.56 CRYST1 61.848 68.775 68.424 90.00 90.35 90.00 C 1 2 1 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 0.016169 0.000000 0.000099 0.00000 SCALE2 0.000000 0.014540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014615 0.00000