HEADER HYDROLASE/DNA 01-AUG-22 8DWD TITLE ADENINE GLYCOSYLASE MUTY VARIANT E43S IN COMPLEX WITH DNA CONTAINING TITLE 2 D(8-OXO-G) PAIRED WITH AN AP SITE GENERATED BY THE ENZYME ACTING ON TITLE 3 PURINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*TP*GP*TP*CP*CP*AP*(ORP)P*GP*TP*CP*T)-3'); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); 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 PROTEIN-DNA COMPLEX, DNA REPAIR, BASE EXCISION REPAIR, KEYWDS 2 APURINIC/APYRIMIDINIC, HYDROLASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.P.RUSSELBURG,M.DEMIR,S.S.DAVID,M.P.HORVATH REVDAT 2 22-MAY-24 8DWD 1 REMARK REVDAT 1 09-AUG-23 8DWD 0 JRNL AUTH L.P.RUSSELBURG,M.DEMIR,K.CEDENO,S.S.DAVID,M.P.HORVATH JRNL TITL STRUCTURAL BASIS FOR BASE ENGAGEMENT AND STEREOCHEMISTRY JRNL TITL 2 REVEALED BY ALTERATION OF CATALYTIC RESIDUE GLU43 IN DNA JRNL TITL 3 REPAIR GLYCOSYLASE MUTY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 100379 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.510 REMARK 3 FREE R VALUE TEST SET COUNT : 2520 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 42.9600 - 4.4000 1.00 5470 139 0.1834 0.2082 REMARK 3 2 4.4000 - 3.4900 1.00 5468 124 0.1742 0.1689 REMARK 3 3 3.4900 - 3.0500 1.00 5474 131 0.1918 0.2290 REMARK 3 4 3.0500 - 2.7700 1.00 5443 141 0.2388 0.2893 REMARK 3 5 2.7700 - 2.5700 1.00 5476 142 0.2369 0.2438 REMARK 3 6 2.5700 - 2.4200 1.00 5435 143 0.2485 0.2423 REMARK 3 7 2.4200 - 2.3000 1.00 5458 143 0.2471 0.2452 REMARK 3 8 2.3000 - 2.2000 1.00 5376 160 0.2551 0.3014 REMARK 3 9 2.2000 - 2.1200 1.00 5478 140 0.2506 0.2732 REMARK 3 10 2.1200 - 2.0400 1.00 5446 139 0.2701 0.3293 REMARK 3 11 2.0400 - 1.9800 1.00 5425 139 0.2933 0.3128 REMARK 3 12 1.9800 - 1.9200 1.00 5476 133 0.3070 0.3447 REMARK 3 13 1.9200 - 1.8700 0.99 5378 144 0.3123 0.3408 REMARK 3 14 1.8700 - 1.8300 1.00 5484 148 0.3156 0.2945 REMARK 3 15 1.8300 - 1.7900 0.99 5363 144 0.3128 0.3403 REMARK 3 16 1.7900 - 1.7500 0.99 5463 129 0.3378 0.3558 REMARK 3 17 1.7500 - 1.7100 0.99 5312 140 0.3565 0.3410 REMARK 3 18 1.7100 - 1.6800 0.98 5434 141 0.3887 0.3905 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.363 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.79 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 : 0.008 3270 REMARK 3 ANGLE : 1.029 4566 REMARK 3 CHIRALITY : 0.052 512 REMARK 3 PLANARITY : 0.009 512 REMARK 3 DIHEDRAL : 17.523 1214 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ((CHAIN A) AND (RESID 8:228 OR RESID 401 OR RESID REMARK 3 403)) REMARK 3 ORIGIN FOR THE GROUP (A): 12.8498 2.2993 3.0368 REMARK 3 T TENSOR REMARK 3 T11: 0.2413 T22: 0.3252 REMARK 3 T33: 0.1902 T12: 0.0673 REMARK 3 T13: 0.0533 T23: 0.0143 REMARK 3 L TENSOR REMARK 3 L11: 2.9597 L22: 0.9656 REMARK 3 L33: 0.4343 L12: -0.3768 REMARK 3 L13: -0.4041 L23: -0.2623 REMARK 3 S TENSOR REMARK 3 S11: 0.2682 S12: 1.5266 S13: 0.1693 REMARK 3 S21: -0.1603 S22: -0.1942 S23: -0.0350 REMARK 3 S31: -0.1063 S32: -0.0956 S33: -0.0334 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ((CHAIN A) AND (RESID 229:360 OR RESID 402 OR RESID REMARK 3 404)) REMARK 3 ORIGIN FOR THE GROUP (A): 20.7826 7.7026 37.3313 REMARK 3 T TENSOR REMARK 3 T11: 0.4886 T22: 0.5682 REMARK 3 T33: 0.3499 T12: -0.0381 REMARK 3 T13: -0.0573 T23: -0.1286 REMARK 3 L TENSOR REMARK 3 L11: 0.4036 L22: 0.0826 REMARK 3 L33: 0.1864 L12: 0.0420 REMARK 3 L13: -0.0042 L23: 0.0011 REMARK 3 S TENSOR REMARK 3 S11: 0.0768 S12: -0.6105 S13: 0.3288 REMARK 3 S21: 0.2530 S22: 0.0991 S23: -0.2565 REMARK 3 S31: 0.0341 S32: 0.3959 S33: 0.0026 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ((CHAIN B AND RESID 1:11) OR (CHAIN C AND RESID REMARK 3 12:22)) REMARK 3 ORIGIN FOR THE GROUP (A): 20.1470 -3.9945 16.1449 REMARK 3 T TENSOR REMARK 3 T11: 0.3600 T22: 0.2550 REMARK 3 T33: 0.3428 T12: 0.0121 REMARK 3 T13: -0.0067 T23: 0.0203 REMARK 3 L TENSOR REMARK 3 L11: 0.2315 L22: 0.3263 REMARK 3 L33: 0.1580 L12: -0.2705 REMARK 3 L13: 0.0442 L23: 0.0025 REMARK 3 S TENSOR REMARK 3 S11: 0.0714 S12: 0.0078 S13: -0.3084 REMARK 3 S21: -0.1166 S22: -0.1290 S23: -0.1337 REMARK 3 S31: 0.3501 S32: 0.1392 S33: 0.0000 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 8DWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267480. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 100381 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 43.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.760 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.90000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6U7T REMARK 200 REMARK 200 REMARK: YELLOW, HEXAGONAL ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, CALCIUM ACETATE, ETHYLENE REMARK 280 GLYCOL, TRIS-HCL, BETA-MERCAPTOETHANOL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K 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 18.87000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.34500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.96000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.34500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.87000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.96000 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: 5570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 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 MET A 1 REMARK 465 THR A 2 REMARK 465 ARG A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 ARG A 7 REMARK 465 GLY A 275 REMARK 465 ALA A 276 REMARK 465 GLN A 289 REMARK 465 TYR A 290 REMARK 465 GLY A 291 REMARK 465 LEU A 292 REMARK 465 GLN A 293 REMARK 465 GLY A 361 REMARK 465 VAL A 362 REMARK 465 ARG A 363 REMARK 465 ARG A 364 REMARK 465 PRO A 365 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 PHE A 8 N CA CB CG CD1 CD2 CE1 REMARK 470 PHE A 8 CE2 CZ REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 ARG A 15 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 52 CG CD OE1 OE2 REMARK 470 ASP A 75 CG OD1 OD2 REMARK 470 GLU A 76 CG CD OE1 OE2 REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 ARG A 167 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 172 CG CD OE1 NE2 REMARK 470 GLU A 176 CG CD OE1 OE2 REMARK 470 ARG A 201 CD NE CZ NH1 NH2 REMARK 470 ARG A 202 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 219 CG CD OE1 OE2 REMARK 470 LYS A 228 CD CE NZ REMARK 470 MET A 229 CG SD CE REMARK 470 LYS A 230 CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 LYS A 235 CD CE NZ REMARK 470 ASP A 277 CG OD1 OD2 REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 GLN A 284 CG CD OE1 NE2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 VAL A 294 N CA CB CG1 CG2 REMARK 470 GLU A 295 CG CD OE1 OE2 REMARK 470 ARG A 320 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 328 CG CD OE1 OE2 REMARK 470 LYS A 356 CD CE NZ REMARK 470 DT C 12 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT C 12 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT C 12 C7 C6 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 OP2 DT C 22 O HOH C 101 1.97 REMARK 500 O HOH B 111 O HOH B 127 2.14 REMARK 500 OE1 GLU A 267 O HOH A 501 2.14 REMARK 500 O HOH B 129 O HOH B 130 2.15 REMARK 500 OE2 GLU A 188 O HOH A 502 2.16 REMARK 500 O HOH A 513 O HOH A 606 2.16 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 OE2 GLU A 59 O3' DT C 22 1455 2.13 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 CYS A 198 CA - CB - SG ANGL. DEV. = 8.9 DEGREES REMARK 500 DA B 2 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC C 16 O4' - C1' - N1 ANGL. DEV. = 3.8 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 ARG A 34 39.85 -99.78 REMARK 500 TYR A 88 69.12 33.55 REMARK 500 PRO A 139 49.45 -79.60 REMARK 500 VAL A 197 -57.07 -120.82 REMARK 500 ARG A 202 61.21 37.94 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 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 118 O REMARK 620 2 SER A 118 OG 70.7 REMARK 620 3 VAL A 123 O 94.2 99.2 REMARK 620 4 HOH A 521 O 63.4 133.9 80.2 REMARK 620 5 HOH A 524 O 143.7 73.2 87.3 151.5 REMARK 620 6 HOH A 618 O 80.5 80.5 174.5 96.0 97.9 REMARK 620 7 HOH C 107 O 130.1 137.0 113.5 80.8 81.0 69.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 198 SG REMARK 620 2 SF4 A 401 S1 120.9 REMARK 620 3 SF4 A 401 S2 110.0 103.7 REMARK 620 4 SF4 A 401 S4 111.4 104.5 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 198 SG REMARK 620 2 SF4 A 401 S1 106.6 REMARK 620 3 SF4 A 401 S2 127.7 104.6 REMARK 620 4 SF4 A 401 S4 107.3 104.4 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 SF4 A 401 S1 118.2 REMARK 620 3 SF4 A 401 S3 109.1 104.2 REMARK 620 4 SF4 A 401 S4 115.7 104.6 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 SF4 A 401 S1 103.0 REMARK 620 3 SF4 A 401 S3 122.6 103.9 REMARK 620 4 SF4 A 401 S4 116.0 104.2 104.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 SF4 A 401 S2 112.0 REMARK 620 3 SF4 A 401 S3 118.4 104.3 REMARK 620 4 SF4 A 401 S4 112.2 105.7 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 SF4 A 401 S2 140.1 REMARK 620 3 SF4 A 401 S3 107.7 104.4 REMARK 620 4 SF4 A 401 S4 89.7 104.8 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 214 SG REMARK 620 2 SF4 A 401 S1 110.0 REMARK 620 3 SF4 A 401 S2 120.7 104.1 REMARK 620 4 SF4 A 401 S3 112.1 104.2 104.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 214 SG REMARK 620 2 SF4 A 401 S1 81.6 REMARK 620 3 SF4 A 401 S2 139.6 104.3 REMARK 620 4 SF4 A 401 S3 113.6 103.9 103.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 404 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 259 O REMARK 620 2 THR A 259 OG1 66.7 REMARK 620 3 HOH A 638 O 151.5 140.0 REMARK 620 N 1 2 DBREF 8DWD A 1 365 UNP P83847 MUTY_GEOSE 1 365 DBREF 8DWD B 1 11 PDB 8DWD 8DWD 1 11 DBREF 8DWD C 12 22 PDB 8DWD 8DWD 12 22 SEQADV 8DWD SER A 43 UNP P83847 GLU 43 ENGINEERED MUTATION SEQRES 1 A 365 MET THR ARG GLU THR GLU ARG PHE PRO ALA ARG GLU PHE SEQRES 2 A 365 GLN ARG ASP LEU LEU ASP TRP PHE ALA ARG GLU ARG ARG SEQRES 3 A 365 ASP LEU PRO TRP ARG LYS ASP ARG ASP PRO TYR LYS VAL SEQRES 4 A 365 TRP VAL SER SER VAL MET LEU GLN GLN THR ARG VAL GLU SEQRES 5 A 365 THR VAL ILE PRO TYR PHE GLU GLN PHE ILE ASP ARG PHE SEQRES 6 A 365 PRO THR LEU GLU ALA LEU ALA ASP ALA ASP GLU ASP GLU SEQRES 7 A 365 VAL LEU LYS ALA TRP GLU GLY LEU GLY TYR TYR SER ARG SEQRES 8 A 365 VAL ARG ASN LEU HIS ALA ALA VAL LYS GLU VAL LYS THR SEQRES 9 A 365 ARG TYR GLY GLY LYS VAL PRO ASP ASP PRO ASP GLU PHE SEQRES 10 A 365 SER ARG LEU LYS GLY VAL GLY PRO TYR THR VAL GLY ALA SEQRES 11 A 365 VAL LEU SER LEU ALA TYR GLY VAL PRO GLU PRO ALA VAL SEQRES 12 A 365 ASP GLY ASN VAL MET ARG VAL LEU SER ARG LEU PHE LEU SEQRES 13 A 365 VAL THR ASP ASP ILE ALA LYS PRO SER THR ARG LYS ARG SEQRES 14 A 365 PHE GLU GLN ILE VAL ARG GLU ILE MET ALA TYR GLU ASN SEQRES 15 A 365 PRO GLY ALA PHE ASN GLU ALA LEU ILE GLU LEU GLY ALA SEQRES 16 A 365 LEU VAL CYS THR PRO ARG ARG PRO SER CYS LEU LEU CYS SEQRES 17 A 365 PRO VAL GLN ALA TYR CYS GLN ALA PHE ALA GLU GLY VAL SEQRES 18 A 365 ALA GLU GLU LEU PRO VAL LYS MET LYS LYS THR ALA VAL SEQRES 19 A 365 LYS GLN VAL PRO LEU ALA VAL ALA VAL LEU ALA ASP ASP SEQRES 20 A 365 GLU GLY ARG VAL LEU ILE ARG LYS ARG ASP SER THR GLY SEQRES 21 A 365 LEU LEU ALA ASN LEU TRP GLU PHE PRO SER CYS GLU THR SEQRES 22 A 365 ASP GLY ALA ASP GLY LYS GLU LYS LEU GLU GLN MET VAL SEQRES 23 A 365 GLY GLU GLN TYR GLY LEU GLN VAL GLU LEU THR GLU PRO SEQRES 24 A 365 ILE VAL SER PHE GLU HIS ALA PHE SER HIS LEU VAL TRP SEQRES 25 A 365 GLN LEU THR VAL PHE PRO GLY ARG LEU VAL HIS GLY GLY SEQRES 26 A 365 PRO VAL GLU GLU PRO TYR ARG LEU ALA PRO GLU ASP GLU SEQRES 27 A 365 LEU LYS ALA TYR ALA PHE PRO VAL SER HIS GLN ARG VAL SEQRES 28 A 365 TRP ARG GLU TYR LYS GLU TRP ALA SER GLY VAL ARG ARG SEQRES 29 A 365 PRO SEQRES 1 B 11 DA DA DG DA DC 8OG DT DG DG DA DC SEQRES 1 C 11 DT DG DT DC DC DA ORP DG DT DC DT HET 8OG B 6 34 HET ORP C 18 20 HET SF4 A 401 16 HET ACT A 402 7 HET CA A 403 1 HET CA A 404 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM ACT ACETATE ION HETNAM CA CALCIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 3 ORP C5 H11 O7 P FORMUL 4 SF4 FE4 S4 FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 CA 2(CA 2+) FORMUL 8 HOH *214(H2 O) HELIX 1 AA1 PRO A 9 ARG A 25 1 17 HELIX 2 AA2 LEU A 28 LYS A 32 5 5 HELIX 3 AA3 ASP A 35 LEU A 46 1 12 HELIX 4 AA4 ARG A 50 PHE A 65 1 16 HELIX 5 AA5 THR A 67 ASP A 73 1 7 HELIX 6 AA6 ASP A 75 GLU A 84 1 10 HELIX 7 AA7 TYR A 89 ARG A 105 1 17 HELIX 8 AA8 ASP A 113 ARG A 119 1 7 HELIX 9 AA9 GLY A 124 TYR A 136 1 13 HELIX 10 AB1 ASP A 144 PHE A 155 1 12 HELIX 11 AB2 LYS A 163 MET A 178 1 16 HELIX 12 AB3 ASN A 182 VAL A 197 1 16 HELIX 13 AB4 VAL A 210 TYR A 213 5 4 HELIX 14 AB5 CYS A 214 GLY A 220 1 7 HELIX 15 AB6 VAL A 221 LEU A 225 5 5 HELIX 16 AB7 GLY A 278 GLU A 288 1 11 HELIX 17 AB8 ASP A 337 TYR A 342 5 6 HELIX 18 AB9 PRO A 345 SER A 360 1 16 SHEET 1 AA1 4 SER A 270 GLU A 272 0 SHEET 2 AA1 4 LYS A 235 ALA A 245 -1 N ALA A 240 O CYS A 271 SHEET 3 AA1 4 LEU A 310 ARG A 320 1 O PHE A 317 N VAL A 241 SHEET 4 AA1 4 GLU A 295 LEU A 296 -1 N GLU A 295 O ARG A 320 SHEET 1 AA2 4 SER A 270 GLU A 272 0 SHEET 2 AA2 4 LYS A 235 ALA A 245 -1 N ALA A 240 O CYS A 271 SHEET 3 AA2 4 LEU A 310 ARG A 320 1 O PHE A 317 N VAL A 241 SHEET 4 AA2 4 VAL A 301 ALA A 306 -1 N PHE A 303 O LEU A 314 SHEET 1 AA3 3 TRP A 266 GLU A 267 0 SHEET 2 AA3 3 ARG A 250 LYS A 255 -1 N ARG A 254 O GLU A 267 SHEET 3 AA3 3 TYR A 331 PRO A 335 -1 O ALA A 334 N VAL A 251 LINK O3' DC B 5 P 8OG B 6 1555 1555 1.60 LINK O3' 8OG B 6 P DT B 7 1555 1555 1.60 LINK O3' DA C 17 P ORP C 18 1555 1555 1.60 LINK O3 ORP C 18 P DG C 19 1555 1555 1.59 LINK O SER A 118 CA CA A 403 1555 1555 2.43 LINK OG SER A 118 CA CA A 403 1555 1555 2.25 LINK O VAL A 123 CA CA A 403 1555 1555 2.26 LINK SG ACYS A 198 FE3 ASF4 A 401 1555 1555 2.25 LINK SG BCYS A 198 FE3 BSF4 A 401 1555 1555 2.29 LINK SG ACYS A 205 FE2 ASF4 A 401 1555 1555 2.28 LINK SG BCYS A 205 FE2 BSF4 A 401 1555 1555 2.27 LINK SG ACYS A 208 FE1 ASF4 A 401 1555 1555 2.31 LINK SG BCYS A 208 FE1 BSF4 A 401 1555 1555 2.19 LINK SG ACYS A 214 FE4 ASF4 A 401 1555 1555 2.30 LINK SG BCYS A 214 FE4 BSF4 A 401 1555 1555 2.26 LINK O THR A 259 CA CA A 404 1555 1555 2.23 LINK OG1 THR A 259 CA CA A 404 1555 1555 2.59 LINK CA CA A 403 O HOH A 521 1555 1555 2.69 LINK CA CA A 403 O HOH A 524 1555 1555 2.02 LINK CA CA A 403 O HOH A 618 1555 1555 2.52 LINK CA CA A 403 O HOH C 107 1555 1555 2.32 LINK CA CA A 404 O HOH A 638 1555 1555 2.73 CISPEP 1 LEU A 225 PRO A 226 0 -0.99 CISPEP 2 GLU A 329 PRO A 330 0 4.78 CRYST1 37.740 85.920 140.690 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 0.026497 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011639 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007108 0.00000