HEADER HYDROLASE/DNA 29-JUL-22 8DVP TITLE GLYCOSYLASE MUTY VARIANT N146S IN COMPLEX WITH DNA CONTAINING D(8-OXO- TITLE 2 G) PAIRED WITH SUBSTRATE PURINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OXOG:A-SPECIFIC ADENINE GLYCOSYLASE; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*TP*GP*TP*CP*CP*AP*(PRN)P*GP*TP*CP*T)-3'); COMPND 13 CHAIN: C; COMPND 14 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: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-DNA COMPLEX, DNA REPAIR, BASE EXCISION REPAIR, HYDROLASE, KEYWDS 2 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.DEMIR,L.P.RUSSELBURG,M.P.HORVATH,S.S.DAVID REVDAT 3 25-OCT-23 8DVP 1 REMARK REVDAT 2 03-MAY-23 8DVP 1 JRNL REVDAT 1 30-NOV-22 8DVP 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. 1.54 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 130279 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.510 REMARK 3 FREE R VALUE TEST SET COUNT : 3269 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 73.4900 - 4.3800 1.00 5564 141 0.1738 0.1854 REMARK 3 2 4.3800 - 3.4800 1.00 5531 124 0.1652 0.1907 REMARK 3 3 3.4800 - 3.0400 1.00 5566 138 0.1882 0.2352 REMARK 3 4 3.0400 - 2.7600 1.00 5559 138 0.2272 0.2356 REMARK 3 5 2.7600 - 2.5600 1.00 5535 145 0.2289 0.2049 REMARK 3 6 2.5600 - 2.4100 1.00 5545 145 0.2362 0.2233 REMARK 3 7 2.4100 - 2.2900 1.00 5552 150 0.2272 0.2161 REMARK 3 8 2.2900 - 2.1900 1.00 5534 158 0.2434 0.2579 REMARK 3 9 2.1900 - 2.1100 1.00 5520 143 0.2669 0.2453 REMARK 3 10 2.1100 - 2.0300 1.00 5602 147 0.2630 0.3138 REMARK 3 11 2.0300 - 1.9700 1.00 5508 139 0.2639 0.2911 REMARK 3 12 1.9700 - 1.9100 1.00 5599 136 0.2660 0.3093 REMARK 3 13 1.9100 - 1.8600 1.00 5562 148 0.2837 0.3206 REMARK 3 14 1.8600 - 1.8200 1.00 5504 150 0.2913 0.2442 REMARK 3 15 1.8200 - 1.7800 1.00 5571 140 0.2982 0.3378 REMARK 3 16 1.7800 - 1.7400 1.00 5559 148 0.3129 0.3178 REMARK 3 17 1.7400 - 1.7000 1.00 5521 137 0.3215 0.3330 REMARK 3 18 1.7000 - 1.6700 1.00 5620 150 0.3173 0.3408 REMARK 3 19 1.6700 - 1.6400 1.00 5511 139 0.3174 0.2975 REMARK 3 20 1.6400 - 1.6100 1.00 5545 142 0.3296 0.3189 REMARK 3 21 1.6100 - 1.5900 1.00 5562 145 0.3474 0.3465 REMARK 3 22 1.5900 - 1.5600 0.98 5383 133 0.3619 0.4105 REMARK 3 23 1.5600 - 1.5400 0.90 5057 133 0.3996 0.4282 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) : 0.282 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.58 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 : 0.014 3279 REMARK 3 ANGLE : 1.291 4582 REMARK 3 CHIRALITY : 0.076 515 REMARK 3 PLANARITY : 0.012 512 REMARK 3 DIHEDRAL : 17.606 1200 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 OR RESID REMARK 3 403)) REMARK 3 ORIGIN FOR THE GROUP (A): 12.8426 2.1670 2.9297 REMARK 3 T TENSOR REMARK 3 T11: 0.2214 T22: 0.3187 REMARK 3 T33: 0.1917 T12: 0.0571 REMARK 3 T13: 0.0008 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 2.9965 L22: 1.1501 REMARK 3 L33: 0.2941 L12: -0.4174 REMARK 3 L13: -0.2617 L23: -0.0371 REMARK 3 S TENSOR REMARK 3 S11: 0.1759 S12: 0.7804 S13: 0.0222 REMARK 3 S21: -0.1364 S22: -0.1350 S23: -0.0120 REMARK 3 S31: -0.0460 S32: 0.0092 S33: -0.0045 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND (RESID 229:360 OR RESID 404)) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9038 7.6458 37.6306 REMARK 3 T TENSOR REMARK 3 T11: 0.4020 T22: 0.5095 REMARK 3 T33: 0.2846 T12: -0.0030 REMARK 3 T13: -0.0422 T23: -0.0935 REMARK 3 L TENSOR REMARK 3 L11: 0.1524 L22: 0.2909 REMARK 3 L33: 0.3350 L12: -0.0747 REMARK 3 L13: 0.0108 L23: 0.1191 REMARK 3 S TENSOR REMARK 3 S11: 0.0039 S12: -0.3845 S13: 0.1800 REMARK 3 S21: 0.1791 S22: 0.1354 S23: -0.1615 REMARK 3 S31: -0.0090 S32: 0.3226 S33: 0.0003 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ((CHAIN B AND RESID 1:11) OR (CHAIN C AND (RESID REMARK 3 12:22 OR RESID 101))) REMARK 3 ORIGIN FOR THE GROUP (A): 19.9079 -3.8564 15.8812 REMARK 3 T TENSOR REMARK 3 T11: 0.3243 T22: 0.2754 REMARK 3 T33: 0.3145 T12: 0.0087 REMARK 3 T13: -0.0043 T23: 0.0359 REMARK 3 L TENSOR REMARK 3 L11: 0.3716 L22: 0.5713 REMARK 3 L33: 0.0990 L12: -0.3273 REMARK 3 L13: -0.0798 L23: -0.0385 REMARK 3 S TENSOR REMARK 3 S11: -0.0033 S12: -0.1791 S13: -0.2344 REMARK 3 S21: -0.1854 S22: -0.0774 S23: -0.0237 REMARK 3 S31: 0.3079 S32: 0.2340 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 8DVP 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_1000267438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-SEP-19 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 : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11585 REMARK 200 MONOCHROMATOR : WATER-COOLED FLAT DOUBLE SI(111) REMARK 200 KHOZU MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 130827 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 73.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 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: 6U7T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 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 293.15K 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 18.84000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.38500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.08500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.38500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.84000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.08500 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: 5920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 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 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 GLU A 52 CG CD OE1 OE2 REMARK 470 GLU A 59 CD OE1 OE2 REMARK 470 ASP A 75 CG OD1 OD2 REMARK 470 GLU A 76 CG CD OE1 OE2 REMARK 470 ASP A 77 CG OD1 OD2 REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 GLN A 172 CG CD OE1 NE2 REMARK 470 GLU A 176 CG CD OE1 OE2 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 CG SD CE REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 GLU A 248 CG CD OE1 OE2 REMARK 470 ASP A 277 CG OD1 OD2 REMARK 470 LYS A 279 CG CD CE NZ REMARK 470 LYS A 281 CE NZ REMARK 470 GLU A 283 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 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 CG CD OE1 OE2 REMARK 470 ASP A 337 CG OD1 OD2 REMARK 470 LYS A 340 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 O HOH B 103 O HOH B 107 2.03 REMARK 500 O HOH A 543 O HOH A 612 2.10 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 DA C 17 C5' DA C 17 C4' 0.051 REMARK 500 DA C 17 N7 DA C 17 C8 0.064 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. = 14.5 DEGREES REMARK 500 DA B 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT B 7 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA C 17 O4' - C1' - N9 ANGL. DEV. = 7.9 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 PRO A 9 75.83 -69.85 REMARK 500 ASP A 33 -167.72 -161.40 REMARK 500 TYR A 88 68.72 34.72 REMARK 500 ASN A 182 82.26 -152.28 REMARK 500 VAL A 197 -59.39 -126.52 REMARK 500 THR A 273 77.23 -109.20 REMARK 500 ALA A 276 -161.85 -124.62 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 91 0.09 SIDE CHAIN 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 73.7 REMARK 620 3 VAL A 123 O 93.5 90.1 REMARK 620 4 HOH A 545 O 65.3 137.4 81.6 REMARK 620 5 HOH A 558 O 147.4 74.4 93.1 147.3 REMARK 620 6 HOH A 594 O 75.2 92.7 167.1 87.8 99.8 REMARK 620 7 HOH C 205 O 146.5 138.7 94.3 83.7 64.4 92.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 144 OD2 REMARK 620 2 SER A 146 OG 92.6 REMARK 620 3 HOH A 531 O 88.0 79.7 REMARK 620 4 HOH A 556 O 80.8 69.7 146.7 REMARK 620 5 PRN C 18 O4' 75.2 145.9 130.3 76.8 REMARK 620 6 PRN C 18 OP2 147.3 110.4 118.0 85.7 72.8 REMARK 620 7 HOH C 209 O 150.6 73.2 64.5 116.1 130.2 61.5 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 116.3 REMARK 620 3 SF4 A 401 S2 112.0 105.3 REMARK 620 4 SF4 A 401 S4 111.7 103.9 106.9 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 115.5 REMARK 620 3 SF4 A 401 S2 116.3 102.1 REMARK 620 4 SF4 A 401 S4 111.3 105.4 105.0 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 113.8 REMARK 620 3 SF4 A 401 S3 108.1 105.6 REMARK 620 4 SF4 A 401 S4 118.9 105.2 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 SF4 A 401 S1 107.3 REMARK 620 3 SF4 A 401 S3 122.0 105.0 REMARK 620 4 SF4 A 401 S4 110.9 106.1 104.4 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 115.0 REMARK 620 3 SF4 A 401 S3 115.4 106.2 REMARK 620 4 SF4 A 401 S4 108.6 107.2 103.5 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 145.1 REMARK 620 3 SF4 A 401 S3 104.3 104.0 REMARK 620 4 SF4 A 401 S4 86.1 106.4 103.8 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 109.2 REMARK 620 3 SF4 A 401 S2 123.6 104.0 REMARK 620 4 SF4 A 401 S3 109.9 103.6 104.7 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 71.2 REMARK 620 3 SF4 A 401 S2 146.7 105.1 REMARK 620 4 SF4 A 401 S3 108.6 104.3 104.4 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 ASP A 257 OD1 REMARK 620 2 THR A 259 O 71.9 REMARK 620 3 THR A 259 OG1 91.0 70.0 REMARK 620 4 HOH A 506 O 61.4 69.9 136.8 REMARK 620 N 1 2 3 DBREF 8DVP A 1 365 UNP P83847 MUTY_GEOSE 1 365 DBREF 8DVP B 1 11 PDB 8DVP 8DVP 1 11 DBREF 8DVP C 12 22 PDB 8DVP 8DVP 12 22 SEQADV 8DVP 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 PRN DG DT DC DT HET 8OG B 6 34 HET PRN C 18 30 HET SF4 A 401 16 HET ACT A 402 7 HET CA A 403 1 HET CA A 404 1 HET CA C 101 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM PRN PURINE 2'-DEOXYRIBO-5'-MONOPHOSPHATE 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 PRN C10 H13 N4 O6 P FORMUL 4 SF4 FE4 S4 FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 CA 3(CA 2+) FORMUL 9 HOH *180(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 GLN A 47 1 13 HELIX 4 AA4 ARG A 50 PHE A 65 1 16 HELIX 5 AA5 THR A 67 ALA A 74 1 8 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 ASP A 277 GLU A 288 1 12 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 LEU A 321 1 O GLN A 313 N LEU A 239 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 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 LEU A 321 1 O GLN A 313 N LEU A 239 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 1.58 LINK O3' 8OG B 6 P DT B 7 1555 1555 1.62 LINK O3' DA C 17 P PRN C 18 1555 1555 1.61 LINK O3' PRN C 18 P DG C 19 1555 1555 1.63 LINK O SER A 118 CA CA A 403 1555 1555 2.41 LINK OG SER A 118 CA CA A 403 1555 1555 2.40 LINK O VAL A 123 CA CA A 403 1555 1555 2.33 LINK OD2 ASP A 144 CA CA C 101 1555 1555 2.52 LINK OG SER A 146 CA CA C 101 1555 1555 2.45 LINK SG ACYS A 198 FE3 ASF4 A 401 1555 1555 2.33 LINK SG BCYS A 198 FE3 BSF4 A 401 1555 1555 2.29 LINK SG ACYS A 205 FE2 ASF4 A 401 1555 1555 2.32 LINK SG BCYS A 205 FE2 BSF4 A 401 1555 1555 2.28 LINK SG ACYS A 208 FE1 ASF4 A 401 1555 1555 2.29 LINK SG BCYS A 208 FE1 BSF4 A 401 1555 1555 2.16 LINK SG ACYS A 214 FE4 ASF4 A 401 1555 1555 2.28 LINK SG BCYS A 214 FE4 BSF4 A 401 1555 1555 2.31 LINK OD1 ASP A 257 CA CA A 404 1555 1555 2.37 LINK O THR A 259 CA CA A 404 1555 1555 2.46 LINK OG1 THR A 259 CA CA A 404 1555 1555 2.35 LINK CA CA A 403 O HOH A 545 1555 1555 2.56 LINK CA CA A 403 O HOH A 558 1555 1555 2.16 LINK CA CA A 403 O HOH A 594 1555 1555 2.48 LINK CA CA A 403 O HOH C 205 1555 1555 2.20 LINK CA CA A 404 O HOH A 506 1555 1555 2.37 LINK O HOH A 531 CA CA C 101 1555 1555 2.35 LINK O HOH A 556 CA CA C 101 1555 1555 2.38 LINK O4' PRN C 18 CA CA C 101 1555 1555 2.46 LINK OP2 PRN C 18 CA CA C 101 1555 1555 2.29 LINK CA CA C 101 O HOH C 209 1555 1555 2.86 CISPEP 1 LEU A 225 PRO A 226 0 -0.99 CISPEP 2 GLU A 329 PRO A 330 0 0.81 CRYST1 37.680 86.170 140.770 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 0.026539 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007104 0.00000