HEADER HYDROLASE/DNA 31-JUL-22 8DW4 TITLE GLYCOSYLASE MUTY VARIANT N146S IN COMPLEX WITH DNA CONTAINING D(8-OXO- TITLE 2 G) PAIRED WITH AN ABASIC SITE PRODUCT (AP) GENERATED BY THE ENZYME IN TITLE 3 CRYSTALS BY REMOVAL OF CALCIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OXOG:A-SPECIFIC ADENINE GLYCOSYLASE; COMPND 5 EC: 3.2.2.31; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(P*GP*TP*CP*CP*AP*(AAB)P*GP*TP*CP*T)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: MUTY; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); 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 PROTEIN-DNA COMPLEX, DNA REPAIR, APURINIC/APYRIMIDINIC, BASE EXCISION KEYWDS 2 REPAIR, HYDROLASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.DEMIR,L.P.RUSSELBURG,M.P.HORVATH,S.S.DAVID REVDAT 3 25-OCT-23 8DW4 1 REMARK REVDAT 2 03-MAY-23 8DW4 1 JRNL REVDAT 1 30-NOV-22 8DW4 0 JRNL AUTH M.DEMIR,L.P.RUSSELBURG,W.J.LIN,C.H.TRASVINA-ARENAS,B.HUANG, JRNL AUTH 2 P.K.YUEN,M.P.HORVATH,S.S.DAVID JRNL TITL STRUCTURAL SNAPSHOTS OF BASE EXCISION BY THE JRNL TITL 2 CANCER-ASSOCIATED VARIANT MUTY N146S REVEAL A RETAINING JRNL TITL 3 MECHANISM. JRNL REF NUCLEIC ACIDS RES. V. 51 1034 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36631987 JRNL DOI 10.1093/NAR/GKAC1246 REMARK 2 REMARK 2 RESOLUTION. 2.49 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30761 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.450 REMARK 3 FREE R VALUE TEST SET COUNT : 754 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 54.4500 - 4.2600 1.00 5994 145 0.1747 0.2133 REMARK 3 2 4.2600 - 3.3800 1.00 6013 142 0.2049 0.1984 REMARK 3 3 3.3800 - 2.9500 1.00 6027 140 0.2875 0.2750 REMARK 3 4 2.9500 - 2.6800 1.00 5957 171 0.3406 0.3585 REMARK 3 5 2.6800 - 2.4900 1.00 6016 156 0.3589 0.3722 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) : 0.531 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.351 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.93 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 : 0.003 3253 REMARK 3 ANGLE : 0.633 4539 REMARK 3 CHIRALITY : 0.040 509 REMARK 3 PLANARITY : 0.004 510 REMARK 3 DIHEDRAL : 18.634 1198 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 7:228) OR RESID 401) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7147 2.6501 2.8895 REMARK 3 T TENSOR REMARK 3 T11: 0.3809 T22: 0.4777 REMARK 3 T33: 0.3465 T12: 0.0388 REMARK 3 T13: 0.0031 T23: 0.0316 REMARK 3 L TENSOR REMARK 3 L11: 3.9816 L22: 1.8813 REMARK 3 L33: 0.6756 L12: -0.3356 REMARK 3 L13: -0.3164 L23: 0.1663 REMARK 3 S TENSOR REMARK 3 S11: 0.1248 S12: 0.8723 S13: 0.0548 REMARK 3 S21: -0.0867 S22: -0.1246 S23: 0.0401 REMARK 3 S31: -0.0669 S32: -0.0191 S33: -0.0126 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 229:360 REMARK 3 ORIGIN FOR THE GROUP (A): 20.6522 7.7014 37.6631 REMARK 3 T TENSOR REMARK 3 T11: 0.5450 T22: 0.6418 REMARK 3 T33: 0.3897 T12: -0.0201 REMARK 3 T13: -0.0515 T23: -0.1008 REMARK 3 L TENSOR REMARK 3 L11: 1.2922 L22: 1.2983 REMARK 3 L33: 1.0844 L12: -0.2828 REMARK 3 L13: 0.1881 L23: 0.1523 REMARK 3 S TENSOR REMARK 3 S11: 0.1392 S12: -0.4437 S13: 0.3885 REMARK 3 S21: 0.1335 S22: 0.0903 S23: -0.2298 REMARK 3 S31: -0.0397 S32: 0.3127 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (((CHAIN B) AND (RESID 1:11)) OR ((CHAIN C) AND REMARK 3 (RESID 12:22))) REMARK 3 ORIGIN FOR THE GROUP (A): 19.8574 -3.7314 15.9563 REMARK 3 T TENSOR REMARK 3 T11: 0.5718 T22: 0.4072 REMARK 3 T33: 0.6370 T12: 0.0313 REMARK 3 T13: 0.0492 T23: 0.0748 REMARK 3 L TENSOR REMARK 3 L11: 0.9380 L22: 1.2301 REMARK 3 L33: 0.8375 L12: -0.7664 REMARK 3 L13: 0.3441 L23: -0.0428 REMARK 3 S TENSOR REMARK 3 S11: -0.1016 S12: -0.4770 S13: -0.5328 REMARK 3 S21: -0.2071 S22: -0.1198 S23: -0.1574 REMARK 3 S31: 0.5973 S32: 0.4676 S33: -0.0024 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 8DW4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267464. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-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 : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30778 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 54.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 0.0498 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: 8DVP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, CALCIUM ACETATE, ETHYLENE REMARK 280 GLYCOL, TRIS.HCL, B-MERCAPTOETHANOL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298.13K 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 18.82000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.58500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.77500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.58500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.82000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.77500 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: 5540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17440 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 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 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 ARG A 7 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 ARG A 15 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 34 NE CZ NH1 NH2 REMARK 470 ARG A 50 NE CZ NH1 NH2 REMARK 470 GLU A 52 CG CD OE1 OE2 REMARK 470 ASP A 73 CG OD1 OD2 REMARK 470 GLU A 76 CG CD OE1 OE2 REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 LYS A 121 CE NZ REMARK 470 LYS A 163 CE NZ REMARK 470 ARG A 201 CG 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 GLU A 223 CG CD OE1 OE2 REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 MET A 229 SD CE REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 ASP A 277 CG OD1 OD2 REMARK 470 LYS A 279 CG CD CE NZ REMARK 470 GLU A 280 CG CD OE1 OE2 REMARK 470 GLN A 284 CG CD OE1 NE2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 GLN A 293 CG CD OE1 NE2 REMARK 470 VAL A 294 CG1 CG2 REMARK 470 GLU A 295 CG CD OE1 OE2 REMARK 470 GLU A 298 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 GLU A 329 CD OE1 OE2 REMARK 470 ASP A 337 CG OD1 OD2 REMARK 470 LYS A 340 CG CD CE NZ REMARK 470 LYS A 356 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 H GLY A 145 OP2 DG C 19 1.57 REMARK 500 O3P AAB C 18 O HOH C 101 2.10 REMARK 500 O1P AAB C 18 O HOH C 102 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 2.18 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 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.2 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 262 57.18 39.45 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 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 118 O REMARK 620 2 LEU A 120 O 87.6 REMARK 620 3 VAL A 123 O 92.7 85.4 REMARK 620 4 HOH A 517 O 82.2 159.7 77.6 REMARK 620 5 DC C 21 OP1 169.8 83.1 82.3 105.2 REMARK 620 6 HOH C 108 O 99.7 94.7 167.6 104.2 85.5 REMARK 620 N 1 2 3 4 5 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 118.3 REMARK 620 3 SF4 A 401 S2 113.2 104.2 REMARK 620 4 SF4 A 401 S4 111.6 103.9 104.2 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 115.8 REMARK 620 3 SF4 A 401 S3 121.6 104.2 REMARK 620 4 SF4 A 401 S4 105.2 104.0 104.1 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 107.3 REMARK 620 3 SF4 A 401 S3 110.6 104.2 REMARK 620 4 SF4 A 401 S4 124.7 104.2 104.0 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 104.0 REMARK 620 3 SF4 A 401 S2 120.0 104.2 REMARK 620 4 SF4 A 401 S3 118.2 104.2 104.2 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8DVP RELATED DB: PDB DBREF 8DW4 A 1 365 UNP P83847 MUTY_GEOSE 1 365 DBREF 8DW4 B 1 11 PDB 8DW4 8DW4 1 11 DBREF 8DW4 C 12 22 PDB 8DW4 8DW4 12 22 SEQADV 8DW4 SER A 146 UNP P83847 ASN 146 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 GLU 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 SER 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 AAB DG DT DC DT HET 8OG B 6 34 HET AAB C 18 21 HET SF4 A 401 8 HET ACT A 402 7 HET NA A 403 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM AAB 2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM ACT ACETATE ION HETNAM NA SODIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN AAB ABASIC DEOXYRIBOSE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 3 AAB C5 H11 O7 P FORMUL 4 SF4 FE4 S4 FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 NA NA 1+ FORMUL 7 HOH *31(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 TRP A 83 1 9 HELIX 7 AA7 TYR A 89 TYR A 106 1 18 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 CYS A 214 GLY A 220 1 7 HELIX 14 AB5 VAL A 221 LEU A 225 5 5 HELIX 15 AB6 GLY A 278 GLU A 288 1 11 HELIX 16 AB7 ASP A 337 TYR A 342 5 6 HELIX 17 AB8 PRO A 345 SER A 360 1 16 SHEET 1 AA1 4 SER A 270 CYS A 271 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 LEU A 321 1 O VAL A 311 N VAL A 237 SHEET 4 AA1 4 VAL A 294 LEU A 296 -1 N GLU A 295 O ARG A 320 SHEET 1 AA2 4 SER A 270 CYS A 271 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 LEU A 321 1 O VAL A 311 N VAL A 237 SHEET 4 AA2 4 VAL A 301 ALA A 306 -1 N HIS A 305 O TRP A 312 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 AAAB C 18 1555 1555 1.61 LINK O3'AAAB C 18 P A DG C 19 1555 1555 1.61 LINK O3'BAAB C 18 P B DG C 19 1555 1555 1.61 LINK O SER A 118 NA NA A 403 1555 1555 2.55 LINK O LEU A 120 NA NA A 403 1555 1555 2.85 LINK O VAL A 123 NA NA A 403 1555 1555 2.59 LINK SG CYS A 198 FE3 SF4 A 401 1555 1555 2.67 LINK SG CYS A 205 FE2 SF4 A 401 1555 1555 2.27 LINK SG CYS A 208 FE1 SF4 A 401 1555 1555 2.16 LINK SG CYS A 214 FE4 SF4 A 401 1555 1555 2.24 LINK NA NA A 403 O HOH A 517 1555 1555 2.26 LINK NA NA A 403 OP1 DC C 21 1555 1555 2.91 LINK NA NA A 403 O HOH C 108 1555 1555 1.96 CISPEP 1 LEU A 225 PRO A 226 0 2.44 CISPEP 2 GLU A 329 PRO A 330 0 7.84 CRYST1 37.640 85.550 141.170 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 0.026567 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011689 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007084 0.00000