HEADER HYDROLASE 30-JUN-21 7P0W TITLE CRYSTAL STRUCTURE OF A TRAPPED PAB-AGOG/DOUBLE-STANDED DNA COVALENT TITLE 2 INTERMEDIATE (DNA CONTAINING THYMINE 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 OTHER_DETAILS: TTT(PED)TTTCT; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*AP*GP*AP*AP*AP*TP*AP*AP*A)-3'); COMPND 15 CHAIN: I; COMPND 16 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, AGOG, PYROCOCCUS ABYSSI, TRAPPED KEYWDS 2 DOUBLE-STRANDED DNA INTERMEDIATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.COSTE,S.GOFFINONT,D.FLAMENT,B.CASTAING REVDAT 3 31-JAN-24 7P0W 1 REMARK REVDAT 2 11-JAN-23 7P0W 1 JRNL REVDAT 1 13-JUL-22 7P0W 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. 1.12 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) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 114270 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 5802 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 34.6500 - 3.4700 1.00 3847 221 0.1414 0.1476 REMARK 3 2 3.4700 - 2.7500 1.00 3708 207 0.1326 0.1683 REMARK 3 3 2.7500 - 2.4100 1.00 3707 209 0.1265 0.1354 REMARK 3 4 2.4100 - 2.1900 1.00 3677 198 0.1198 0.1294 REMARK 3 5 2.1900 - 2.0300 1.00 3669 176 0.1206 0.1435 REMARK 3 6 2.0300 - 1.9100 1.00 3698 189 0.1219 0.1426 REMARK 3 7 1.9100 - 1.8100 1.00 3644 190 0.1215 0.1279 REMARK 3 8 1.8100 - 1.7400 1.00 3661 177 0.1184 0.1321 REMARK 3 9 1.7400 - 1.6700 1.00 3598 205 0.1138 0.1307 REMARK 3 10 1.6700 - 1.6100 1.00 3627 217 0.1075 0.1411 REMARK 3 11 1.6100 - 1.5600 1.00 3621 211 0.1043 0.1321 REMARK 3 12 1.5600 - 1.5200 1.00 3634 218 0.1022 0.1247 REMARK 3 13 1.5200 - 1.4800 1.00 3644 198 0.1025 0.1255 REMARK 3 14 1.4800 - 1.4400 1.00 3617 175 0.1038 0.1204 REMARK 3 15 1.4400 - 1.4100 1.00 3594 198 0.1064 0.1364 REMARK 3 16 1.4100 - 1.3800 1.00 3634 178 0.1147 0.1439 REMARK 3 17 1.3800 - 1.3500 1.00 3673 177 0.1067 0.1474 REMARK 3 18 1.3500 - 1.3200 1.00 3605 180 0.1070 0.1342 REMARK 3 19 1.3200 - 1.3000 1.00 3586 199 0.1103 0.1469 REMARK 3 20 1.3000 - 1.2800 1.00 3671 184 0.1084 0.1325 REMARK 3 21 1.2800 - 1.2600 1.00 3572 204 0.1057 0.1261 REMARK 3 22 1.2600 - 1.2400 1.00 3590 217 0.1134 0.1317 REMARK 3 23 1.2400 - 1.2200 1.00 3597 209 0.1169 0.1385 REMARK 3 24 1.2200 - 1.2000 1.00 3642 179 0.1192 0.1480 REMARK 3 25 1.2000 - 1.1900 1.00 3650 165 0.1264 0.1580 REMARK 3 26 1.1900 - 1.1700 1.00 3556 200 0.1326 0.1541 REMARK 3 27 1.1700 - 1.1600 0.99 3570 203 0.1429 0.1598 REMARK 3 28 1.1600 - 1.1400 0.97 3503 167 0.1519 0.1971 REMARK 3 29 1.1400 - 1.1300 0.94 3423 171 0.1607 0.1555 REMARK 3 30 1.1300 - 1.1200 0.91 3250 180 0.1761 0.1983 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.22 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 : NULL 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 7P0W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292116767. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-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 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 : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 114280 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 45.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.59800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 7OY7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MGCL2, NA ACETATE PH5.0, MPD, VAPOR REMARK 280 DIFFUSION, HANGING 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 69.34550 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 69.34550 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 29.88800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.78900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.88800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.78900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.34550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.88800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.78900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.34550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.88800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.78900 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: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 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 C3 MPD A 301 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 489 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 CE NZ 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 LYS A 182 CG CD CE NZ REMARK 470 LYS A 188 CD CE NZ REMARK 470 LYS A 191 NZ REMARK 470 LYS A 195 CE NZ REMARK 470 LYS A 230 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 NZ LYS A 142 H1'2 PED B 4 1.32 REMARK 500 O HOH A 667 O HOH A 690 1.96 REMARK 500 O HOH A 529 O HOH B 101 2.00 REMARK 500 O HOH A 627 O HOH A 659 2.06 REMARK 500 OE2 GLU A 173 O HOH A 401 2.06 REMARK 500 O HOH A 642 O HOH A 676 2.08 REMARK 500 O HOH A 409 O HOH A 638 2.09 REMARK 500 O HOH I 640 O HOH I 642 2.10 REMARK 500 O HOH A 496 O HOH A 508 2.14 REMARK 500 O HOH A 476 O HOH A 601 2.16 REMARK 500 O HOH A 636 O HOH A 669 2.18 REMARK 500 O HOH A 610 O HOH A 636 2.19 REMARK 500 O HOH A 643 O HOH A 702 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 656 O HOH A 696 7444 2.08 REMARK 500 OXT ARG A 239 O HOH A 564 5445 2.13 REMARK 500 NE2 HIS A 0 OP2 DA I 9 5545 2.14 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' -0.038 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 DA I 8 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 75 -80.65 -101.11 REMARK 500 ASP A 123 67.23 -150.20 REMARK 500 ASP A 174 -179.53 179.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 101 0.09 SIDE CHAIN 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 726 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A 727 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH B 138 DISTANCE = 6.28 ANGSTROMS 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 NA A 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 129 O REMARK 620 2 HOH A 548 O 139.1 REMARK 620 3 HOH A 623 O 114.7 91.4 REMARK 620 4 HOH A 633 O 105.8 93.0 109.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH I 608 O REMARK 620 2 HOH I 628 O 129.1 REMARK 620 3 HOH I 638 O 68.5 77.5 REMARK 620 N 1 2 DBREF 7P0W A 1 239 UNP Q9UZY0 AGOG_PYRAB 1 239 DBREF 7P0W B 1 9 PDB 7P0W 7P0W 1 9 DBREF 7P0W I 1 9 PDB 7P0W 7P0W 1 9 SEQADV 7P0W GLY A -2 UNP Q9UZY0 EXPRESSION TAG SEQADV 7P0W SER A -1 UNP Q9UZY0 EXPRESSION TAG SEQADV 7P0W 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 DT DA DA DA HET PED B 4 20 HET MPD A 301 22 HET NA A 302 1 HET NA A 303 1 HET MPD I 501 22 HETNAM PED PENTANE-3,4-DIOL-5-PHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM NA SODIUM ION HETSYN PED OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE FORMUL 2 PED C5 H13 O6 P FORMUL 4 MPD 2(C6 H14 O2) FORMUL 5 NA 2(NA 1+) FORMUL 8 HOH *409(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 SER A 88 1 13 HELIX 6 AA6 LEU A 94 THR A 111 1 18 HELIX 7 AA7 THR A 113 GLY A 122 1 10 HELIX 8 AA8 ASP A 123 GLY A 136 1 14 HELIX 9 AA9 SER A 141 SER A 160 1 20 HELIX 10 AB1 ASP A 174 THR A 185 1 12 HELIX 11 AB2 LYS A 188 GLY A 201 1 14 HELIX 12 AB3 PRO A 203 GLY A 216 1 14 HELIX 13 AB4 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 LINK O GLY A 129 NA NA A 302 1555 1555 2.87 LINK NA NA A 302 O HOH A 548 1555 1555 2.92 LINK NA NA A 302 O HOH A 623 1555 1555 2.78 LINK NA NA A 302 O HOH A 633 1555 1555 2.76 LINK NA NA A 303 O HOH I 608 1555 1555 3.10 LINK NA NA A 303 O HOH I 628 1555 1555 2.81 LINK NA NA A 303 O HOH I 638 1555 1555 2.99 CRYST1 59.776 71.578 138.691 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 0.016729 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013971 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007210 0.00000