HEADER HYDROLASE/DNA 12-MAY-24 9BS2 TITLE GLYCOSYLASE MUTY VARIANT R149Q IN COMPLEX WITH DNA CONTAINING D(8-OXO- TITLE 2 G) PAIRED WITH A PRODUCT ANALOG (THF) TO 1.51 A RESOLUTION 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 OTHER_DETAILS: SYNTHETIC DNA; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: SYNTHETIC DNA 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 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-DNA COMPLEX, DNA REPAIR, BASE EXCISION REPAIR, HYDROLASE, KEYWDS 2 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.H.TRASVINA-ARENAS,N.TAMAYO,W.J.LIN,M.DEMIR,A.J.FISHER,S.S.DAVID, AUTHOR 2 M.P.HORVATH REVDAT 1 30-OCT-24 9BS2 0 JRNL AUTH C.H.TRASVINA-ARENAS,U.C.DISSANAYAKE,N.TAMAYO,S.M.HASHEMIAN, JRNL AUTH 2 W.J.LIN,M.DEMIR,N.HOYOS-GONZALEZ,A.J.FISHER,G.A.CISNEROS, JRNL AUTH 3 M.P.HORVATH,S.S.DAVID JRNL TITL STRUCTURAL AND FUNCTIONAL PROFILING OF MUTYH JRNL TITL 2 CANCER-ASSOCIATED VARIANTS REVEAL AN ALLOSTERIC ROLE FOR ITS JRNL TITL 3 [4FE-4S] CLUSTER COFACTOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.51 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 135544 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.520 REMARK 3 FREE R VALUE TEST SET COUNT : 3412 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 43.0000 - 4.3500 1.00 5614 140 0.1648 0.1598 REMARK 3 2 4.3500 - 3.4600 1.00 5570 128 0.1468 0.2056 REMARK 3 3 3.4600 - 3.0200 1.00 5647 137 0.1759 0.2072 REMARK 3 4 3.0200 - 2.7400 1.00 5555 141 0.2008 0.2061 REMARK 3 5 2.7400 - 2.5500 1.00 5619 148 0.2110 0.2186 REMARK 3 6 2.5500 - 2.4000 1.00 5614 145 0.2122 0.2412 REMARK 3 7 2.4000 - 2.2800 1.00 5554 154 0.2188 0.2015 REMARK 3 8 2.2800 - 2.1800 1.00 5583 157 0.2238 0.2608 REMARK 3 9 2.1800 - 2.0900 1.00 5586 141 0.2201 0.2491 REMARK 3 10 2.0900 - 2.0200 1.00 5618 151 0.2375 0.2424 REMARK 3 11 2.0200 - 1.9600 1.00 5543 138 0.2411 0.2525 REMARK 3 12 1.9600 - 1.9000 1.00 5619 143 0.2803 0.3765 REMARK 3 13 1.9000 - 1.8500 0.99 5587 140 0.2699 0.3000 REMARK 3 14 1.8500 - 1.8100 1.00 5585 151 0.2579 0.2789 REMARK 3 15 1.8100 - 1.7700 0.99 5556 139 0.2690 0.2933 REMARK 3 16 1.7700 - 1.7300 1.00 5553 151 0.2755 0.2956 REMARK 3 17 1.7300 - 1.6900 0.98 5520 144 0.2844 0.3227 REMARK 3 18 1.6900 - 1.6600 0.98 5554 139 0.3132 0.3621 REMARK 3 19 1.6600 - 1.6300 0.99 5514 147 0.3313 0.3274 REMARK 3 20 1.6300 - 1.6000 0.97 5471 145 0.3544 0.3812 REMARK 3 21 1.6000 - 1.5800 0.99 5549 137 0.3686 0.4124 REMARK 3 22 1.5800 - 1.5500 0.97 5397 139 0.3831 0.4129 REMARK 3 23 1.5500 - 1.5300 0.92 5210 136 0.4157 0.3929 REMARK 3 24 1.5300 - 1.5100 0.82 4514 121 0.4288 0.4384 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.071 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.81 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 : 0.012 3361 REMARK 3 ANGLE : 1.179 4697 REMARK 3 CHIRALITY : 0.062 526 REMARK 3 PLANARITY : 0.011 533 REMARK 3 DIHEDRAL : 18.157 1239 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND (RESID 8:228)) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4765 2.2326 2.4991 REMARK 3 T TENSOR REMARK 3 T11: 0.1695 T22: 0.2414 REMARK 3 T33: 0.1327 T12: 0.0510 REMARK 3 T13: 0.0127 T23: 0.0269 REMARK 3 L TENSOR REMARK 3 L11: 4.0928 L22: 1.3233 REMARK 3 L33: 0.9286 L12: -0.4589 REMARK 3 L13: -0.4401 L23: -0.2990 REMARK 3 S TENSOR REMARK 3 S11: 0.2170 S12: 0.8517 S13: 0.0800 REMARK 3 S21: -0.1849 S22: -0.1430 S23: -0.0154 REMARK 3 S31: -0.0419 S32: -0.0296 S33: 0.0737 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND (RESID 229:360 OR RESID 402 OR RESID REMARK 3 405)) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6450 7.7616 37.1948 REMARK 3 T TENSOR REMARK 3 T11: 0.3751 T22: 0.4888 REMARK 3 T33: 0.2470 T12: 0.0147 REMARK 3 T13: -0.0317 T23: -0.1082 REMARK 3 L TENSOR REMARK 3 L11: 0.4698 L22: 0.4488 REMARK 3 L33: 0.3561 L12: -0.0788 REMARK 3 L13: 0.2372 L23: -0.0314 REMARK 3 S TENSOR REMARK 3 S11: -0.0145 S12: -0.3958 S13: 0.2231 REMARK 3 S21: 0.2840 S22: 0.1566 S23: -0.2576 REMARK 3 S31: 0.0278 S32: 0.3152 S33: 0.0067 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ((CHAIN B AND RESID 1:11) OR (CHAIN C AND RESID REMARK 3 12:22)) REMARK 3 ORIGIN FOR THE GROUP (A): 19.6888 -4.1258 16.2189 REMARK 3 T TENSOR REMARK 3 T11: 0.2835 T22: 0.2144 REMARK 3 T33: 0.2585 T12: 0.0259 REMARK 3 T13: 0.0108 T23: 0.0423 REMARK 3 L TENSOR REMARK 3 L11: 0.3948 L22: 0.4075 REMARK 3 L33: 0.1618 L12: -0.3242 REMARK 3 L13: 0.1310 L23: 0.0152 REMARK 3 S TENSOR REMARK 3 S11: 0.0319 S12: -0.2770 S13: -0.1748 REMARK 3 S21: -0.1356 S22: -0.0938 S23: -0.0600 REMARK 3 S31: 0.3290 S32: 0.1610 S33: -0.0001 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 9BS2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1000284024. 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 : 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 : 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 : 136096 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 70.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.860 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.37 REMARK 200 R MERGE FOR SHELL (I) : 2.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.510 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: NULL REMARK 200 REMARK 200 REMARK: LARGE 0.2 X 0.3 MM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 14%, 0.4 M CALCIUM ACETATE, 2% REMARK 280 ETHYLENE GLYCOL, PH 8.5, WITH MICROSEED CRYSTALS FROM N146S 10X REMARK 280 STOCK, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K 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 18.75000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.32000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.32000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.75000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.00000 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: 5470 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ARG A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 ARG A 7 REMARK 465 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 PRO A 364 REMARK 465 PRO A 365 REMARK 465 PRO A 366 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 GLU A 12 CG CD OE1 OE2 REMARK 470 ARG A 15 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 32 CE NZ REMARK 470 LYS A 38 CE NZ REMARK 470 GLU A 52 CG CD OE1 OE2 REMARK 470 GLN A 60 CD OE1 NE2 REMARK 470 ARG A 64 NE CZ NH1 NH2 REMARK 470 GLU A 76 CG CD OE1 OE2 REMARK 470 LYS A 163 CE NZ REMARK 470 ARG A 201 CD NE CZ NH1 NH2 REMARK 470 ARG A 202 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 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 LYS A 235 CE NZ REMARK 470 ASP A 274 CG OD1 OD2 REMARK 470 ASP A 277 CG OD1 OD2 REMARK 470 GLU A 280 CG CD OE1 OE2 REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 GLN A 284 CG CD OE1 NE2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 GLN A 289 CG CD OE1 NE2 REMARK 470 GLN A 293 CG CD OE1 NE2 REMARK 470 GLU A 295 CG CD OE1 OE2 REMARK 470 GLU A 298 CG CD OE1 OE2 REMARK 470 ARG A 320 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 328 CG CD OE1 OE2 REMARK 470 GLU A 329 CG CD OE1 OE2 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 OP2 DT C 22 O HOH C 101 1.95 REMARK 500 O HOH B 106 O HOH B 129 2.09 REMARK 500 O HOH A 556 O HOH C 117 2.09 REMARK 500 O HOH A 545 O HOH A 647 2.11 REMARK 500 N7 DA B 1 O HOH B 101 2.12 REMARK 500 N1 DA B 1 O HOH B 102 2.12 REMARK 500 O HOH A 556 O HOH A 666 2.13 REMARK 500 O HOH A 587 O HOH B 123 2.14 REMARK 500 OP1 DT C 14 O HOH C 102 2.16 REMARK 500 N3 DA B 2 O HOH B 103 2.17 REMARK 500 OD2 ASP A 35 O HOH A 501 2.18 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 B 4 O3' DA B 4 C3' -0.038 REMARK 500 DC C 16 O3' DC C 16 C3' -0.052 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 198 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 DA B 1 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC B 5 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 7 C1' - O4' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC C 16 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA C 17 O3' - P - OP2 ANGL. DEV. = 10.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 25 126.19 -38.78 REMARK 500 ARG A 25 126.84 -39.90 REMARK 500 TYR A 88 67.46 39.64 REMARK 500 PRO A 139 47.75 -83.80 REMARK 500 ASP A 144 -169.35 -107.60 REMARK 500 MET A 178 178.07 -53.67 REMARK 500 VAL A 197 -61.60 -123.65 REMARK 500 ARG A 202 58.36 37.52 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 404 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 118 O REMARK 620 2 SER A 118 OG 76.8 REMARK 620 3 VAL A 123 O 91.4 94.2 REMARK 620 4 HOH A 575 O 147.0 70.2 90.1 REMARK 620 5 HOH A 578 O 67.2 143.3 80.3 145.2 REMARK 620 6 HOH A 638 O 80.5 87.9 170.9 98.9 92.7 REMARK 620 7 HOH C 106 O 134.6 140.1 106.4 75.9 75.0 77.0 REMARK 620 N 1 2 3 4 5 6 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 ASN A 146 OD1 REMARK 620 2 GLY A 194 O 71.0 REMARK 620 3 HOH A 576 O 99.6 65.9 REMARK 620 4 HOH A 590 O 120.8 63.7 94.9 REMARK 620 5 HOH C 108 O 150.6 138.3 93.5 83.7 REMARK 620 6 HOH C 110 O 81.1 106.6 171.4 77.6 89.8 REMARK 620 7 HOH C 111 O 77.2 136.7 92.0 159.1 76.1 96.4 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 118.4 REMARK 620 3 SF4 A 401 S2 111.8 103.7 REMARK 620 4 SF4 A 401 S4 113.7 102.9 105.0 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 115.1 REMARK 620 3 SF4 A 401 S2 115.8 104.1 REMARK 620 4 SF4 A 401 S4 111.7 104.4 104.5 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 113.9 REMARK 620 3 SF4 A 401 S3 108.5 104.0 REMARK 620 4 SF4 A 401 S4 121.0 103.8 104.0 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 108.7 REMARK 620 3 SF4 A 401 S3 110.9 105.8 REMARK 620 4 SF4 A 401 S4 121.9 104.7 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 SF4 A 401 S2 112.6 REMARK 620 3 SF4 A 401 S3 119.0 104.5 REMARK 620 4 SF4 A 401 S4 109.9 105.8 103.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 SF4 A 401 S2 124.5 REMARK 620 3 SF4 A 401 S3 110.6 104.0 REMARK 620 4 SF4 A 401 S4 107.1 105.4 103.2 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 111.4 REMARK 620 3 SF4 A 401 S2 116.2 103.8 REMARK 620 4 SF4 A 401 S3 115.3 105.0 104.0 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 88.8 REMARK 620 3 SF4 A 401 S2 132.2 104.8 REMARK 620 4 SF4 A 401 S3 116.6 104.4 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 405 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 257 OD1 REMARK 620 2 ASP A 257 OD2 46.7 REMARK 620 3 THR A 259 O 65.7 111.6 REMARK 620 4 THR A 259 OG1 80.8 114.6 53.7 REMARK 620 5 HOH A 659 O 128.0 86.0 141.9 149.2 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8FAY RELATED DB: PDB REMARK 900 HUMAN MUTYH DBREF 9BS2 A 1 363 UNP P83847 MUTY_GEOSE 1 363 DBREF 9BS2 B 1 11 PDB 9BS2 9BS2 1 11 DBREF 9BS2 C 12 22 PDB 9BS2 9BS2 12 22 SEQADV 9BS2 GLY A -2 UNP P83847 EXPRESSION TAG SEQADV 9BS2 SER A -1 UNP P83847 EXPRESSION TAG SEQADV 9BS2 HIS A 0 UNP P83847 EXPRESSION TAG SEQADV 9BS2 GLN A 149 UNP P83847 ARG 149 ENGINEERED MUTATION SEQADV 9BS2 PRO A 364 UNP P83847 EXPRESSION TAG SEQADV 9BS2 PRO A 365 UNP P83847 EXPRESSION TAG SEQADV 9BS2 PRO A 366 UNP P83847 EXPRESSION TAG SEQRES 1 A 369 GLY SER HIS MET THR ARG GLU THR GLU ARG PHE PRO ALA SEQRES 2 A 369 ARG GLU PHE GLN ARG ASP LEU LEU ASP TRP PHE ALA ARG SEQRES 3 A 369 GLU ARG ARG ASP LEU PRO TRP ARG LYS ASP ARG ASP PRO SEQRES 4 A 369 TYR LYS VAL TRP VAL SER GLU VAL MET LEU GLN GLN THR SEQRES 5 A 369 ARG VAL GLU THR VAL ILE PRO TYR PHE GLU GLN PHE ILE SEQRES 6 A 369 ASP ARG PHE PRO THR LEU GLU ALA LEU ALA ASP ALA ASP SEQRES 7 A 369 GLU ASP GLU VAL LEU LYS ALA TRP GLU GLY LEU GLY TYR SEQRES 8 A 369 TYR SER ARG VAL ARG ASN LEU HIS ALA ALA VAL LYS GLU SEQRES 9 A 369 VAL LYS THR ARG TYR GLY GLY LYS VAL PRO ASP ASP PRO SEQRES 10 A 369 ASP GLU PHE SER ARG LEU LYS GLY VAL GLY PRO TYR THR SEQRES 11 A 369 VAL GLY ALA VAL LEU SER LEU ALA TYR GLY VAL PRO GLU SEQRES 12 A 369 PRO ALA VAL ASP GLY ASN VAL MET GLN VAL LEU SER ARG SEQRES 13 A 369 LEU PHE LEU VAL THR ASP ASP ILE ALA LYS PRO SER THR SEQRES 14 A 369 ARG LYS ARG PHE GLU GLN ILE VAL ARG GLU ILE MET ALA SEQRES 15 A 369 TYR GLU ASN PRO GLY ALA PHE ASN GLU ALA LEU ILE GLU SEQRES 16 A 369 LEU GLY ALA LEU VAL CYS THR PRO ARG ARG PRO SER CYS SEQRES 17 A 369 LEU LEU CYS PRO VAL GLN ALA TYR CYS GLN ALA PHE ALA SEQRES 18 A 369 GLU GLY VAL ALA GLU GLU LEU PRO VAL LYS MET LYS LYS SEQRES 19 A 369 THR ALA VAL LYS GLN VAL PRO LEU ALA VAL ALA VAL LEU SEQRES 20 A 369 ALA ASP ASP GLU GLY ARG VAL LEU ILE ARG LYS ARG ASP SEQRES 21 A 369 SER THR GLY LEU LEU ALA ASN LEU TRP GLU PHE PRO SER SEQRES 22 A 369 CYS GLU THR ASP GLY ALA ASP GLY LYS GLU LYS LEU GLU SEQRES 23 A 369 GLN MET VAL GLY GLU GLN TYR GLY LEU GLN VAL GLU LEU SEQRES 24 A 369 THR GLU PRO ILE VAL SER PHE GLU HIS ALA PHE SER HIS SEQRES 25 A 369 LEU VAL TRP GLN LEU THR VAL PHE PRO GLY ARG LEU VAL SEQRES 26 A 369 HIS GLY GLY PRO VAL GLU GLU PRO TYR ARG LEU ALA PRO SEQRES 27 A 369 GLU ASP GLU LEU LYS ALA TYR ALA PHE PRO VAL SER HIS SEQRES 28 A 369 GLN ARG VAL TRP ARG GLU TYR LYS GLU TRP ALA SER GLY SEQRES 29 A 369 VAL ARG PRO 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 3DR DG DT DC DT HET 8OG B 6 34 HET 3DR C 18 19 HET SF4 A 401 16 HET ACY A 402 7 HET CA A 403 1 HET CA A 404 1 HET CA A 405 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM ACY ACETIC ACID HETNAM CA CALCIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 3 3DR C5 H11 O6 P FORMUL 4 SF4 FE4 S4 FORMUL 5 ACY C2 H4 O2 FORMUL 6 CA 3(CA 2+) FORMUL 9 HOH *241(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 GLU A 84 1 10 HELIX 7 AA7 TYR A 89 GLY A 107 1 19 HELIX 8 AA8 ASP A 113 ARG A 119 1 7 HELIX 9 AA9 GLY A 124 GLY A 137 1 14 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 208 TYR A 213 5 6 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 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 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 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 VAL A 311 N VAL A 237 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 1.60 LINK O3' DA C 17 P 3DR C 18 1555 1555 1.57 LINK O3' 3DR C 18 P DG C 19 1555 1555 1.61 LINK O SER A 118 CA CA A 404 1555 1555 2.42 LINK OG SER A 118 CA CA A 404 1555 1555 2.49 LINK O VAL A 123 CA CA A 404 1555 1555 2.33 LINK OD1 ASN A 146 CA CA A 403 1555 1555 2.29 LINK O GLY A 194 CA CA A 403 1555 1555 2.83 LINK SG ACYS A 198 FE3 ASF4 A 401 1555 1555 2.33 LINK SG BCYS A 198 FE3 BSF4 A 401 1555 1555 2.20 LINK SG ACYS A 205 FE2 ASF4 A 401 1555 1555 2.23 LINK SG BCYS A 205 FE2 BSF4 A 401 1555 1555 2.24 LINK SG ACYS A 208 FE1 ASF4 A 401 1555 1555 2.28 LINK SG BCYS A 208 FE1 BSF4 A 401 1555 1555 2.24 LINK SG ACYS A 214 FE4 ASF4 A 401 1555 1555 2.30 LINK SG BCYS A 214 FE4 BSF4 A 401 1555 1555 2.26 LINK OD1 ASP A 257 CA CA A 405 1555 1555 2.27 LINK OD2 ASP A 257 CA CA A 405 1555 1555 3.01 LINK O THR A 259 CA CA A 405 1555 1555 2.96 LINK OG1 THR A 259 CA CA A 405 1555 1555 2.12 LINK CA CA A 403 O HOH A 576 1555 1555 2.35 LINK CA CA A 403 O HOH A 590 1555 1555 2.40 LINK CA CA A 403 O HOH C 108 1555 1555 2.26 LINK CA CA A 403 O HOH C 110 1555 1555 2.45 LINK CA CA A 403 O HOH C 111 1555 1555 2.39 LINK CA CA A 404 O HOH A 575 1555 1555 2.24 LINK CA CA A 404 O HOH A 578 1555 1555 2.54 LINK CA CA A 404 O HOH A 638 1555 1555 2.33 LINK CA CA A 404 O HOH C 106 1555 1555 2.22 LINK CA CA A 405 O HOH A 659 1555 1555 2.50 CISPEP 1 LEU A 225 PRO A 226 0 -1.09 CISPEP 2 GLU A 329 PRO A 330 0 3.85 CRYST1 37.500 86.000 140.640 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 0.026667 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011628 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007110 0.00000