PDB Short entry for 6U7T HEADER HYDROLASE/DNA 03-SEP-19 6U7T TITLE MUTY ADENINE GLYCOSYLASE BOUND TO DNA CONTAINING A TRANSITION STATE TITLE 2 ANALOG (1N) PAIRED WITH D(8-OXO-G) 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 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(P*GP*TP*CP*CP*AP*(NR1)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 GENE: MUTY; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; 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, TRANSITION STATE ANALOG, HYDROLASE- KEYWDS 2 DNA COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.L.O'SHEA MURRAY,S.CAO,M.P.HORVATH,S.S.DAVID REVDAT 6 29-JAN-20 6U7T 1 JRNL REVDAT 5 25-DEC-19 6U7T 1 JRNL ATOM REVDAT 4 27-NOV-19 6U7T 1 REMARK REVDAT 3 20-NOV-19 6U7T 1 LINK REVDAT 2 13-NOV-19 6U7T 1 JRNL REVDAT 1 02-OCT-19 6U7T 0 SPRSDE 02-OCT-19 6U7T 5DPK JRNL AUTH L.P.RUSSELBURG,V.L.O'SHEA MURRAY,M.DEMIR,K.R.KNUTSEN, JRNL AUTH 2 S.L.SEHGAL,S.CAO,S.S.DAVID,M.P.HORVATH JRNL TITL STRUCTURAL BASIS FOR FINDING OG LESIONS AND AVOIDING JRNL TITL 2 UNDAMAGED G BY THE DNA GLYCOSYLASE MUTY. JRNL REF ACS CHEM.BIOL. V. 15 93 2020 JRNL REFN ESSN 1554-8937 JRNL PMID 31829624 JRNL DOI 10.1021/ACSCHEMBIO.9B00639 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.D.WOODS,V.L.O'SHEA,A.CHU,S.CAO,J.L.RICHARDS,M.P.HORVATH, REMARK 1 AUTH 2 S.S.DAVID REMARK 1 TITL STRUCTURE AND STEREOCHEMISTRY OF THE BASE EXCISION REPAIR REMARK 1 TITL 2 GLYCOSYLASE MUTY REVEAL A MECHANISM SIMILAR TO RETAINING REMARK 1 TITL 3 GLYCOSIDASES. REMARK 1 REF NUCLEIC ACIDS RES. V. 44 801 2016 REMARK 1 REFN ESSN 1362-4962 REMARK 1 PMID 26673696 REMARK 1 DOI 10.1093/NAR/GKV1469 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15RC2_3428 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 30194 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.262 REMARK 3 R VALUE (WORKING SET) : 0.261 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1456 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 41.3340 - 4.3074 1.00 3264 156 0.2094 0.2147 REMARK 3 2 4.3074 - 3.4194 1.00 3097 146 0.2191 0.2266 REMARK 3 3 3.4194 - 2.9873 1.00 3078 148 0.2593 0.2427 REMARK 3 4 2.9873 - 2.7142 0.99 2997 163 0.2977 0.3168 REMARK 3 5 2.7142 - 2.5197 0.99 3008 149 0.3081 0.2871 REMARK 3 6 2.5197 - 2.3712 0.99 2988 153 0.3205 0.3222 REMARK 3 7 2.3712 - 2.2524 0.98 2935 170 0.3397 0.3654 REMARK 3 8 2.2524 - 2.1544 0.97 2915 147 0.3624 0.3945 REMARK 3 9 2.1544 - 2.0715 0.83 2488 125 0.3720 0.4024 REMARK 3 10 2.0715 - 2.0000 0.66 1968 99 0.3803 0.4199 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.07 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 : 0.005 3300 REMARK 3 ANGLE : 0.735 4584 REMARK 3 CHIRALITY : 0.045 505 REMARK 3 PLANARITY : 0.004 522 REMARK 3 DIHEDRAL : 19.239 1898 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 6U7T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000244120. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 12.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1158 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30197 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 41.334 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 6.523 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.64 REMARK 200 R MERGE FOR SHELL (I) : 1.00800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1RRQ REMARK 200 REMARK 200 REMARK: DARK GOLDEN-BROWN ROD 75 MICROMETER X 350 MICROMETER REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MICRO-SEEDED, 0.5 M CALCIUM ACETATE, REMARK 280 0.1 M TRIS, 14% W/V PEG4000, 0.005 M BETA-MERCAPTOETHANOL, 5% W/ REMARK 280 V ETHYLENE GLYCOL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 18.90000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.29000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.24500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.29000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.24500 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: 5180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18380 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 TYR A 290 REMARK 465 GLY A 291 REMARK 465 LEU A 292 REMARK 465 GLN A 293 REMARK 465 VAL A 294 REMARK 465 GLY A 361 REMARK 465 VAL A 362 REMARK 465 ARG A 363 REMARK 465 PRO A 364 REMARK 465 PRO A 365 REMARK 465 PRO A 366 REMARK 465 DT C 12 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 ARG A 15 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 52 CG CD OE1 OE2 REMARK 470 LYS A 103 CE NZ REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 ARG A 202 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 LYS A 231 CG CD CE NZ 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 GLN A 289 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 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 OD2 ASP A 159 HH22 ARG A 169 1.59 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 HZ3 LYS A 230 OE2 GLU A 248 3645 1.57 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. = 2.0 DEGREES REMARK 500 DC C 16 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA C 17 C3' - O3' - P ANGL. DEV. = 18.1 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 TYR A 88 66.31 39.99 REMARK 500 VAL A 197 -66.74 -105.06 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 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 118 O REMARK 620 2 SER A 118 OG 80.3 REMARK 620 3 VAL A 123 O 86.3 91.1 REMARK 620 4 HOH A 507 O 58.4 135.9 73.0 REMARK 620 5 HOH A 538 O 156.1 76.4 99.3 145.5 REMARK 620 6 HOH A 545 O 70.9 116.0 139.7 66.8 115.1 REMARK 620 7 HOH C 103 O 135.8 143.9 91.2 78.7 67.7 83.7 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 125.2 REMARK 620 3 SF4 A 401 S2 104.2 106.8 REMARK 620 4 SF4 A 401 S4 112.5 101.9 104.5 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 100.9 REMARK 620 3 SF4 A 401 S3 135.0 102.6 REMARK 620 4 SF4 A 401 S4 105.6 101.0 106.8 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 116.2 REMARK 620 3 SF4 A 401 S3 111.7 105.0 REMARK 620 4 SF4 A 401 S4 114.7 102.2 105.8 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 87.5 REMARK 620 3 SF4 A 401 S2 146.0 106.2 REMARK 620 4 SF4 A 401 S3 103.8 102.4 103.4 REMARK 620 N 1 2 3 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 ASP A 257 OD2 REMARK 620 2 THR A 259 O 83.9 REMARK 620 3 THR A 259 OG1 87.0 70.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Q0C RELATED DB: PDB REMARK 900 6Q0C IS THE TSAC STRUCTURE COMPLEX WITH 1N OPPOSITE UNDAMAGED G DBREF 6U7T A 1 366 UNP P83847 MUTY_GEOSE 1 366 DBREF 6U7T B 1 11 PDB 6U7T 6U7T 1 11 DBREF 6U7T C 12 22 PDB 6U7T 6U7T 12 22 SEQADV 6U7T PRO A 364 UNP P83847 ARG 364 VARIANT SEQADV 6U7T PRO A 366 UNP P83847 ASP 366 VARIANT SEQRES 1 A 366 MET THR ARG GLU THR GLU ARG PHE PRO ALA ARG GLU PHE SEQRES 2 A 366 GLN ARG ASP LEU LEU ASP TRP PHE ALA ARG GLU ARG ARG SEQRES 3 A 366 ASP LEU PRO TRP ARG LYS ASP ARG ASP PRO TYR LYS VAL SEQRES 4 A 366 TRP VAL SER GLU VAL MET LEU GLN GLN THR ARG VAL GLU SEQRES 5 A 366 THR VAL ILE PRO TYR PHE GLU GLN PHE ILE ASP ARG PHE SEQRES 6 A 366 PRO THR LEU GLU ALA LEU ALA ASP ALA ASP GLU ASP GLU SEQRES 7 A 366 VAL LEU LYS ALA TRP GLU GLY LEU GLY TYR TYR SER ARG SEQRES 8 A 366 VAL ARG ASN LEU HIS ALA ALA VAL LYS GLU VAL LYS THR SEQRES 9 A 366 ARG TYR GLY GLY LYS VAL PRO ASP ASP PRO ASP GLU PHE SEQRES 10 A 366 SER ARG LEU LYS GLY VAL GLY PRO TYR THR VAL GLY ALA SEQRES 11 A 366 VAL LEU SER LEU ALA TYR GLY VAL PRO GLU PRO ALA VAL SEQRES 12 A 366 ASP GLY ASN VAL MET ARG VAL LEU SER ARG LEU PHE LEU SEQRES 13 A 366 VAL THR ASP ASP ILE ALA LYS PRO SER THR ARG LYS ARG SEQRES 14 A 366 PHE GLU GLN ILE VAL ARG GLU ILE MET ALA TYR GLU ASN SEQRES 15 A 366 PRO GLY ALA PHE ASN GLU ALA LEU ILE GLU LEU GLY ALA SEQRES 16 A 366 LEU VAL CYS THR PRO ARG ARG PRO SER CYS LEU LEU CYS SEQRES 17 A 366 PRO VAL GLN ALA TYR CYS GLN ALA PHE ALA GLU GLY VAL SEQRES 18 A 366 ALA GLU GLU LEU PRO VAL LYS MET LYS LYS THR ALA VAL SEQRES 19 A 366 LYS GLN VAL PRO LEU ALA VAL ALA VAL LEU ALA ASP ASP SEQRES 20 A 366 GLU GLY ARG VAL LEU ILE ARG LYS ARG ASP SER THR GLY SEQRES 21 A 366 LEU LEU ALA ASN LEU TRP GLU PHE PRO SER CYS GLU THR SEQRES 22 A 366 ASP GLY ALA ASP GLY LYS GLU LYS LEU GLU GLN MET VAL SEQRES 23 A 366 GLY GLU GLN TYR GLY LEU GLN VAL GLU LEU THR GLU PRO SEQRES 24 A 366 ILE VAL SER PHE GLU HIS ALA PHE SER HIS LEU VAL TRP SEQRES 25 A 366 GLN LEU THR VAL PHE PRO GLY ARG LEU VAL HIS GLY GLY SEQRES 26 A 366 PRO VAL GLU GLU PRO TYR ARG LEU ALA PRO GLU ASP GLU SEQRES 27 A 366 LEU LYS ALA TYR ALA PHE PRO VAL SER HIS GLN ARG VAL SEQRES 28 A 366 TRP ARG GLU TYR LYS GLU TRP ALA SER GLY VAL ARG PRO SEQRES 29 A 366 PRO 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 NR1 DG DT DC DT HET 8OG B 6 34 HET NR1 C 18 21 HET SF4 A 401 8 HET CA A 402 1 HET CA A 403 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM NR1 (3R,4R)-3-HYDROXY-4-[(PHOSPHONOOXY)METHYL]PYRROLIDINIUM HETNAM SF4 IRON/SULFUR CLUSTER 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 NR1 C5 H13 N O5 P 1+ FORMUL 4 SF4 FE4 S4 FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *75(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 ALA A 74 1 8 HELIX 6 AA6 ASP A 75 TRP A 83 1 9 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 LEU A 156 1 13 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 GLN A 289 1 13 HELIX 17 AB8 PRO A 335 TYR A 342 5 8 HELIX 18 AB9 PRO A 345 ALA A 359 1 15 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 GLN A 313 N LEU A 239 SHEET 4 AA1 4 SER A 302 ALA A 306 -1 N HIS A 305 O TRP A 312 SHEET 1 AA2 3 TRP A 266 GLU A 267 0 SHEET 2 AA2 3 VAL A 251 LYS A 255 -1 N ARG A 254 O GLU A 267 SHEET 3 AA2 3 TYR A 331 ALA A 334 -1 O ALA A 334 N VAL A 251 LINK O SER A 118 CA CA A 402 1555 1555 2.71 LINK OG SER A 118 CA CA A 402 1555 1555 2.66 LINK O VAL A 123 CA CA A 402 1555 1555 2.43 LINK SG CYS A 198 FE3 SF4 A 401 1555 1555 2.29 LINK SG CYS A 205 FE2 SF4 A 401 1555 1555 2.32 LINK SG CYS A 208 FE1 SF4 A 401 1555 1555 2.33 LINK SG CYS A 214 FE4 SF4 A 401 1555 1555 2.35 LINK OD2 ASP A 257 CA CA A 403 1555 1555 2.31 LINK O THR A 259 CA CA A 403 1555 1555 2.30 LINK OG1 THR A 259 CA CA A 403 1555 1555 2.29 LINK O3' DC B 5 P 8OG B 6 1555 1555 1.61 LINK O3' 8OG B 6 P DT B 7 1555 1555 1.60 LINK O3' DA C 17 P NR1 C 18 1555 1555 1.56 LINK O3' NR1 C 18 P DG C 19 1555 1555 1.60 LINK CA CA A 402 O HOH A 507 1555 1555 2.31 LINK CA CA A 402 O HOH A 538 1555 1555 2.28 LINK CA CA A 402 O HOH A 545 1555 1555 3.19 LINK CA CA A 402 O HOH C 103 1555 1555 2.24 CISPEP 1 LEU A 225 PRO A 226 0 2.26 CISPEP 2 GLU A 329 PRO A 330 0 1.56 SITE 1 AC1 6 CYS A 198 CYS A 205 CYS A 208 GLN A 211 SITE 2 AC1 6 CYS A 214 ALA A 222 SITE 1 AC2 5 SER A 118 VAL A 123 HOH A 507 HOH A 538 SITE 2 AC2 5 HOH C 103 SITE 1 AC3 2 ASP A 257 THR A 259 CRYST1 37.800 86.490 140.580 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 0.026455 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007113 0.00000