HEADER DNA BINDING PROTEIN/DNA 21-MAR-21 7EF9 TITLE CRYSTAL STRUCTURE OF MOUSE MUTYH IN COMPLEX WITH DNA CONTAINING AP TITLE 2 SITE ANALOGUE:8-OXOG (FORM II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MUTY HOMOLOG,MMYH; COMPND 5 EC: 3.2.2.31; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*AP*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)- COMPND 9 3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MUTYH, MYH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS DNA REPAIR, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAMURA,Y.NAKABEPPU,Y.YAMAGATA REVDAT 3 21-JUL-21 7EF9 1 JRNL REVDAT 2 07-JUL-21 7EF9 1 JRNL REVDAT 1 23-JUN-21 7EF9 0 JRNL AUTH T.NAKAMURA,K.OKABE,S.HIRAYAMA,M.CHIRIFU,S.IKEMIZU,H.MORIOKA, JRNL AUTH 2 Y.NAKABEPPU,Y.YAMAGATA JRNL TITL STRUCTURE OF THE MAMMALIAN ADENINE DNA GLYCOSYLASE MUTYH: JRNL TITL 2 INSIGHTS INTO THE BASE EXCISION REPAIR PATHWAY AND CANCER. JRNL REF NUCLEIC ACIDS RES. V. 49 7154 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 34142156 JRNL DOI 10.1093/NAR/GKAB492 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : GEOSDT + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 43974 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2222 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 42.5300 - 4.9500 1.00 2783 155 0.1739 0.1957 REMARK 3 2 4.9500 - 3.9300 1.00 2646 170 0.1458 0.1557 REMARK 3 3 3.9300 - 3.4300 1.00 2653 134 0.1674 0.1738 REMARK 3 4 3.4300 - 3.1200 1.00 2647 126 0.1825 0.1871 REMARK 3 5 3.1200 - 2.9000 1.00 2638 133 0.1970 0.2103 REMARK 3 6 2.9000 - 2.7300 0.99 2620 141 0.1981 0.2234 REMARK 3 7 2.7300 - 2.5900 0.99 2605 137 0.1951 0.2184 REMARK 3 8 2.5900 - 2.4800 0.99 2584 140 0.1828 0.2438 REMARK 3 9 2.4800 - 2.3800 0.99 2576 152 0.1812 0.2454 REMARK 3 10 2.3800 - 2.3000 0.99 2593 145 0.1868 0.2202 REMARK 3 11 2.3000 - 2.2300 0.99 2565 142 0.1870 0.2299 REMARK 3 12 2.2300 - 2.1600 0.99 2587 139 0.1925 0.2551 REMARK 3 13 2.1600 - 2.1100 0.99 2589 121 0.2064 0.2464 REMARK 3 14 2.1100 - 2.0600 0.99 2569 119 0.2158 0.2516 REMARK 3 15 2.0600 - 2.0100 0.99 2580 129 0.2317 0.2535 REMARK 3 16 2.0100 - 1.9700 0.96 2517 139 0.2607 0.3085 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.228 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.955 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.03 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 : 0.006 4033 REMARK 3 ANGLE : 0.832 5619 REMARK 3 CHIRALITY : 0.050 611 REMARK 3 PLANARITY : 0.005 633 REMARK 3 DIHEDRAL : 18.823 1506 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 86:200 ) REMARK 3 ORIGIN FOR THE GROUP (A): 74.0775 15.6920 31.5637 REMARK 3 T TENSOR REMARK 3 T11: 0.2900 T22: 0.3220 REMARK 3 T33: 0.2851 T12: -0.0318 REMARK 3 T13: 0.0512 T23: -0.0536 REMARK 3 L TENSOR REMARK 3 L11: 2.1392 L22: 4.4338 REMARK 3 L33: 1.4353 L12: -0.4372 REMARK 3 L13: 0.0232 L23: -0.8142 REMARK 3 S TENSOR REMARK 3 S11: 0.1261 S12: -0.0812 S13: 0.0056 REMARK 3 S21: 0.1565 S22: 0.0307 S23: 0.0127 REMARK 3 S31: -0.1612 S32: -0.1109 S33: -0.1591 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND ((RESID 52:79) OR (RESID 201:331)) REMARK 3 ORIGIN FOR THE GROUP (A): 101.8926 16.9637 20.6626 REMARK 3 T TENSOR REMARK 3 T11: 0.3420 T22: 0.5334 REMARK 3 T33: 0.5598 T12: -0.0310 REMARK 3 T13: 0.0852 T23: -0.0478 REMARK 3 L TENSOR REMARK 3 L11: 1.3134 L22: 1.2277 REMARK 3 L33: 4.7509 L12: 0.6949 REMARK 3 L13: -1.8100 L23: -1.1552 REMARK 3 S TENSOR REMARK 3 S11: 0.1036 S12: 0.2313 S13: 0.0416 REMARK 3 S21: -0.1646 S22: -0.1194 S23: -0.4221 REMARK 3 S31: -0.1498 S32: 0.4658 S33: 0.0166 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 332:470) REMARK 3 ORIGIN FOR THE GROUP (A): 60.8014 40.7243 16.8158 REMARK 3 T TENSOR REMARK 3 T11: 0.4647 T22: 0.3486 REMARK 3 T33: 0.3579 T12: 0.0993 REMARK 3 T13: 0.0909 T23: 0.0760 REMARK 3 L TENSOR REMARK 3 L11: 3.6017 L22: 2.7973 REMARK 3 L33: 4.5856 L12: -0.5234 REMARK 3 L13: -0.8953 L23: 0.1429 REMARK 3 S TENSOR REMARK 3 S11: 0.2720 S12: 0.4856 S13: 0.4304 REMARK 3 S21: -0.4521 S22: 0.0000 S23: 0.1348 REMARK 3 S31: -0.6388 S32: -0.3481 S33: -0.2242 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 82.0444 27.1398 15.3420 REMARK 3 T TENSOR REMARK 3 T11: 0.5027 T22: 0.5347 REMARK 3 T33: 0.6901 T12: 0.0713 REMARK 3 T13: 0.1221 T23: -0.0703 REMARK 3 L TENSOR REMARK 3 L11: 3.0127 L22: 7.5207 REMARK 3 L33: 6.4217 L12: 2.0594 REMARK 3 L13: 1.5271 L23: -0.6974 REMARK 3 S TENSOR REMARK 3 S11: 0.4292 S12: 0.5576 S13: 0.0138 REMARK 3 S21: -0.3621 S22: 0.0787 S23: -1.6164 REMARK 3 S31: 0.5854 S32: 0.8718 S33: -0.2950 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): 83.1940 28.0885 15.9874 REMARK 3 T TENSOR REMARK 3 T11: 0.7151 T22: 0.4404 REMARK 3 T33: 0.7599 T12: -0.0542 REMARK 3 T13: 0.0549 T23: 0.0606 REMARK 3 L TENSOR REMARK 3 L11: 3.2678 L22: 1.9158 REMARK 3 L33: 4.9695 L12: 0.1510 REMARK 3 L13: -0.2659 L23: -2.0025 REMARK 3 S TENSOR REMARK 3 S11: -0.0740 S12: 0.3577 S13: 1.2909 REMARK 3 S21: -1.0271 S22: -0.2702 S23: 0.1610 REMARK 3 S31: -0.7621 S32: 0.1837 S33: 0.3826 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 7EF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021173. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-17 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43985 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 42.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.57600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, LITHIUM SULFATE, AMMONIUM REMARK 280 SULFATE, BIS-TRIS, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.83000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.24800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 79.26350 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.83000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.24800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.26350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.83000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.24800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.26350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.83000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.24800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.26350 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: 7100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -135.0 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 GLY A 40 REMARK 465 PRO A 41 REMARK 465 GLY A 42 REMARK 465 TYR A 43 REMARK 465 GLN A 44 REMARK 465 GLU A 45 REMARK 465 GLU A 46 REMARK 465 LEU A 47 REMARK 465 LEU A 48 REMARK 465 ALA A 290 REMARK 465 LEU A 291 REMARK 465 PRO A 292 REMARK 465 GLY A 293 REMARK 465 ARG A 294 REMARK 465 PRO A 295 REMARK 465 ASP A 296 REMARK 465 ILE A 297 REMARK 465 GLY A 471 REMARK 465 THR A 472 REMARK 465 ARG A 473 REMARK 465 LYS A 474 REMARK 465 GLY A 475 REMARK 465 SER A 476 REMARK 465 LYS A 477 REMARK 465 ARG A 478 REMARK 465 SER A 479 REMARK 465 GLN A 480 REMARK 465 VAL A 481 REMARK 465 CYS A 482 REMARK 465 PRO A 483 REMARK 465 PRO A 484 REMARK 465 SER A 485 REMARK 465 SER A 486 REMARK 465 ARG A 487 REMARK 465 DA C 14 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 GLN A 49 CG CD OE1 NE2 REMARK 470 GLN A 287 CG CD OE1 NE2 REMARK 470 LEU A 288 CG CD1 CD2 REMARK 470 SER A 289 OG 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 7 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 13 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 SER A 51 49.06 -97.72 REMARK 500 PHE A 58 79.32 -104.16 REMARK 500 TYR A 150 70.13 44.19 REMARK 500 VAL A 260 -58.35 -125.65 REMARK 500 GLN A 287 89.30 -68.40 REMARK 500 ASN A 303 57.85 -93.82 REMARK 500 ALA A 350 -129.47 -119.90 REMARK 500 PRO A 401 94.32 -69.35 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 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 56 NE2 REMARK 620 2 CYS A 300 SG 113.9 REMARK 620 3 CYS A 307 SG 156.7 77.9 REMARK 620 4 CYS A 310 SG 154.4 87.0 10.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 261 SG REMARK 620 2 SF4 A 501 S1 118.2 REMARK 620 3 SF4 A 501 S3 110.8 104.3 REMARK 620 4 SF4 A 501 S4 113.0 104.5 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 268 SG REMARK 620 2 SF4 A 501 S1 113.9 REMARK 620 3 SF4 A 501 S2 110.1 104.8 REMARK 620 4 SF4 A 501 S3 118.2 104.5 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 271 SG REMARK 620 2 SF4 A 501 S2 116.8 REMARK 620 3 SF4 A 501 S3 113.6 103.5 REMARK 620 4 SF4 A 501 S4 112.0 105.6 104.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 277 SG REMARK 620 2 SF4 A 501 S1 110.9 REMARK 620 3 SF4 A 501 S2 119.8 104.2 REMARK 620 4 SF4 A 501 S4 109.6 105.3 105.9 REMARK 620 N 1 2 3 DBREF 7EF9 A 45 487 UNP Q99P21 MUTYH_MOUSE 45 487 DBREF 7EF9 B 1 14 PDB 7EF9 7EF9 1 14 DBREF 7EF9 C 1 14 PDB 7EF9 7EF9 1 14 SEQADV 7EF9 GLY A 40 UNP Q99P21 EXPRESSION TAG SEQADV 7EF9 PRO A 41 UNP Q99P21 EXPRESSION TAG SEQADV 7EF9 GLY A 42 UNP Q99P21 EXPRESSION TAG SEQADV 7EF9 TYR A 43 UNP Q99P21 EXPRESSION TAG SEQADV 7EF9 GLN A 44 UNP Q99P21 EXPRESSION TAG SEQRES 1 A 448 GLY PRO GLY TYR GLN GLU GLU LEU LEU GLN ALA SER VAL SEQRES 2 A 448 SER PRO TYR HIS LEU PHE SER ASP VAL ALA ASP VAL THR SEQRES 3 A 448 ALA PHE ARG SER ASN LEU LEU SER TRP TYR ASP GLN GLU SEQRES 4 A 448 LYS ARG ASP LEU PRO TRP ARG ASN LEU ALA LYS GLU GLU SEQRES 5 A 448 ALA ASN SER ASP ARG ARG ALA TYR ALA VAL TRP VAL SER SEQRES 6 A 448 GLU VAL MET LEU GLN GLN THR GLN VAL ALA THR VAL ILE SEQRES 7 A 448 ASP TYR TYR THR ARG TRP MET GLN LYS TRP PRO LYS LEU SEQRES 8 A 448 GLN ASP LEU ALA SER ALA SER LEU GLU GLU VAL ASN GLN SEQRES 9 A 448 LEU TRP SER GLY LEU GLY TYR TYR SER ARG GLY ARG ARG SEQRES 10 A 448 LEU GLN GLU GLY ALA ARG LYS VAL VAL GLU GLU LEU GLY SEQRES 11 A 448 GLY HIS MET PRO ARG THR ALA GLU THR LEU GLN GLN LEU SEQRES 12 A 448 LEU PRO GLY VAL GLY ARG TYR THR ALA GLY ALA ILE ALA SEQRES 13 A 448 SER ILE ALA PHE ASP GLN VAL THR GLY VAL VAL ASP GLY SEQRES 14 A 448 ASN VAL LEU ARG VAL LEU CYS ARG VAL ARG ALA ILE GLY SEQRES 15 A 448 ALA ASP PRO THR SER THR LEU VAL SER HIS HIS LEU TRP SEQRES 16 A 448 ASN LEU ALA GLN GLN LEU VAL ASP PRO ALA ARG PRO GLY SEQRES 17 A 448 ASP PHE ASN GLN ALA ALA MET GLU LEU GLY ALA THR VAL SEQRES 18 A 448 CYS THR PRO GLN ARG PRO LEU CYS SER HIS CYS PRO VAL SEQRES 19 A 448 GLN SER LEU CYS ARG ALA TYR GLN ARG VAL GLN ARG GLY SEQRES 20 A 448 GLN LEU SER ALA LEU PRO GLY ARG PRO ASP ILE GLU GLU SEQRES 21 A 448 CYS ALA LEU ASN THR ARG GLN CYS GLN LEU CYS LEU THR SEQRES 22 A 448 SER SER SER PRO TRP ASP PRO SER MET GLY VAL ALA ASN SEQRES 23 A 448 PHE PRO ARG LYS ALA SER ARG ARG PRO PRO ARG GLU GLU SEQRES 24 A 448 TYR SER ALA THR CYS VAL VAL GLU GLN PRO GLY ALA ILE SEQRES 25 A 448 GLY GLY PRO LEU VAL LEU LEU VAL GLN ARG PRO ASP SER SEQRES 26 A 448 GLY LEU LEU ALA GLY LEU TRP GLU PHE PRO SER VAL THR SEQRES 27 A 448 LEU GLU PRO SER GLU GLN HIS GLN HIS LYS ALA LEU LEU SEQRES 28 A 448 GLN GLU LEU GLN ARG TRP CYS GLY PRO LEU PRO ALA ILE SEQRES 29 A 448 ARG LEU GLN HIS LEU GLY GLU VAL ILE HIS ILE PHE SER SEQRES 30 A 448 HIS ILE LYS LEU THR TYR GLN VAL TYR SER LEU ALA LEU SEQRES 31 A 448 ASP GLN ALA PRO ALA SER THR ALA PRO PRO GLY ALA ARG SEQRES 32 A 448 TRP LEU THR TRP GLU GLU PHE CYS ASN ALA ALA VAL SER SEQRES 33 A 448 THR ALA MET LYS LYS VAL PHE ARG MET TYR GLU ASP HIS SEQRES 34 A 448 ARG GLN GLY THR ARG LYS GLY SER LYS ARG SER GLN VAL SEQRES 35 A 448 CYS PRO PRO SER SER ARG SEQRES 1 B 14 DA DT DG DA DG DA DC 8OG DG DG DG DA DC SEQRES 2 B 14 DT SEQRES 1 C 14 DT DA DG DT DC DC DC 3DR DG DT DC DT DC SEQRES 2 C 14 DA HET 8OG B 8 23 HET 3DR C 8 11 HET SF4 A 501 8 HET ZN A 502 1 HET SO4 A 503 5 HET GOL A 504 6 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET SO4 A 508 5 HET SO4 A 509 5 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 3 3DR C5 H11 O6 P FORMUL 4 SF4 FE4 S4 FORMUL 5 ZN ZN 2+ FORMUL 6 SO4 6(O4 S 2-) FORMUL 7 GOL C3 H8 O3 FORMUL 13 HOH *235(H2 O) HELIX 1 AA1 SER A 53 LEU A 57 5 5 HELIX 2 AA2 ASP A 60 LYS A 79 1 20 HELIX 3 AA3 LEU A 82 GLU A 91 1 10 HELIX 4 AA4 ASN A 93 GLN A 109 1 17 HELIX 5 AA5 GLN A 112 TRP A 127 1 16 HELIX 6 AA6 LYS A 129 SER A 135 1 7 HELIX 7 AA7 SER A 137 SER A 146 1 10 HELIX 8 AA8 TYR A 151 LEU A 168 1 18 HELIX 9 AA9 THR A 175 LEU A 183 1 9 HELIX 10 AB1 GLY A 187 ASP A 200 1 14 HELIX 11 AB2 ASP A 207 ARG A 218 1 12 HELIX 12 AB3 SER A 226 VAL A 241 1 16 HELIX 13 AB4 ARG A 245 VAL A 260 1 16 HELIX 14 AB5 LEU A 267 CYS A 271 5 5 HELIX 15 AB6 VAL A 273 LEU A 276 5 4 HELIX 16 AB7 CYS A 277 GLN A 284 1 8 HELIX 17 AB8 ASP A 318 PHE A 326 5 9 HELIX 18 AB9 GLU A 379 GLN A 383 5 5 HELIX 19 AC1 HIS A 386 GLY A 398 1 13 HELIX 20 AC2 PRO A 401 LEU A 405 5 5 HELIX 21 AC3 THR A 445 ASN A 451 1 7 HELIX 22 AC4 SER A 455 ARG A 469 1 15 SHEET 1 AA1 5 TRP A 371 GLU A 372 0 SHEET 2 AA1 5 LEU A 355 GLN A 360 -1 N VAL A 359 O GLU A 372 SHEET 3 AA1 5 ARG A 336 GLN A 347 -1 N GLN A 347 O LEU A 355 SHEET 4 AA1 5 ILE A 418 ALA A 428 1 O LYS A 419 N ARG A 336 SHEET 5 AA1 5 GLN A 406 ILE A 414 -1 N HIS A 413 O LEU A 420 SHEET 1 AA2 4 SER A 375 LEU A 378 0 SHEET 2 AA2 4 ARG A 336 GLN A 347 -1 N ALA A 341 O VAL A 376 SHEET 3 AA2 4 LEU A 355 GLN A 360 -1 O LEU A 355 N GLN A 347 SHEET 4 AA2 4 ALA A 441 LEU A 444 -1 O ARG A 442 N LEU A 358 LINK O3' DC B 7 P 8OG B 8 1555 1555 1.61 LINK O3' 8OG B 8 P DG B 9 1555 1555 1.60 LINK O3' DC C 7 P 3DR C 8 1555 1555 1.62 LINK O3' 3DR C 8 P DG C 9 1555 1555 1.61 LINK NE2 HIS A 56 ZN ZN A 502 1555 1555 2.11 LINK SG CYS A 261 FE2 SF4 A 501 1555 1555 2.33 LINK SG CYS A 268 FE4 SF4 A 501 1555 1555 2.30 LINK SG CYS A 271 FE1 SF4 A 501 1555 1555 2.31 LINK SG CYS A 277 FE3 SF4 A 501 1555 1555 2.32 LINK SG CYS A 300 ZN ZN A 502 1555 1555 2.36 LINK SG CYS A 307 ZN ZN A 502 1555 3855 2.25 LINK SG CYS A 310 ZN ZN A 502 1555 3855 2.14 CISPEP 1 PHE A 326 PRO A 327 0 -6.75 CISPEP 2 GLY A 353 PRO A 354 0 0.35 CRYST1 71.660 108.496 158.527 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013955 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009217 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006308 0.00000