HEADER DNA BINDING PROTEIN/DNA 08-JAN-18 6C2E OBSLTE 28-MAR-18 6C2E 6CNQ TITLE MBD2 IN COMPLEX WITH METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEMETHYLASE,DMTASE,METHYL-CPG-BINDING PROTEIN MBD2; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 12-MER DNA; COMPND 8 CHAIN: D, C, E, F; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MBD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 OTHER_DETAILS: SYNTHETIC KEYWDS DNA METHYLATION, DNA BINDING, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.LIU,C.XU,W.TEMPEL,C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,J.MIN, AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 28-MAR-18 6C2E 1 OBSLTE REVDAT 1 14-FEB-18 6C2E 0 JRNL AUTH K.LIU,C.XU,W.TEMPEL,C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS, JRNL AUTH 2 J.MIN,STRUCTURAL GENOMICS CONSORTIUM JRNL TITL MBD2 IN COMPLEX WITH METHYLATED DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 40239 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.470 REMARK 3 FREE R VALUE TEST SET COUNT : 1398 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 24.3457 - 4.6242 0.98 3836 134 0.1399 0.1373 REMARK 3 2 4.6242 - 3.6745 1.00 3843 140 0.1664 0.1516 REMARK 3 3 3.6745 - 3.2112 0.98 3935 84 0.2119 0.2927 REMARK 3 4 3.2112 - 2.9181 1.00 3833 140 0.2799 0.3490 REMARK 3 5 2.9181 - 2.7092 1.00 3830 196 0.3117 0.3943 REMARK 3 6 2.7092 - 2.5497 1.00 3848 200 0.2944 0.3256 REMARK 3 7 2.5497 - 2.4221 1.00 4078 0 0.2910 0.0000 REMARK 3 8 2.4221 - 2.3168 1.00 3860 232 0.3016 0.3011 REMARK 3 9 2.3168 - 2.2276 1.00 4028 0 0.3092 0.0000 REMARK 3 10 2.2276 - 2.1508 1.00 3750 272 0.3105 0.3202 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.72 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 : 0.008 2186 REMARK 3 ANGLE : 1.232 3167 REMARK 3 CHIRALITY : 0.068 336 REMARK 3 PLANARITY : 0.008 238 REMARK 3 DIHEDRAL : 26.280 1129 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 34.7308 20.5884 -4.7480 REMARK 3 T TENSOR REMARK 3 T11: 0.8314 T22: 0.4907 REMARK 3 T33: 0.4214 T12: 0.0278 REMARK 3 T13: -0.0286 T23: 0.0387 REMARK 3 L TENSOR REMARK 3 L11: 0.1588 L22: 0.3635 REMARK 3 L33: 0.2379 L12: 0.1028 REMARK 3 L13: 0.0947 L23: 0.1575 REMARK 3 S TENSOR REMARK 3 S11: 0.1042 S12: 0.0605 S13: -0.1811 REMARK 3 S21: -0.1168 S22: 0.0389 S23: 0.2239 REMARK 3 S31: 0.3776 S32: -0.5680 S33: -0.0005 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 28.3411 10.5780 -30.4517 REMARK 3 T TENSOR REMARK 3 T11: 0.6334 T22: 0.7165 REMARK 3 T33: 0.4938 T12: 0.0478 REMARK 3 T13: -0.0397 T23: 0.0369 REMARK 3 L TENSOR REMARK 3 L11: 0.2065 L22: 0.1867 REMARK 3 L33: 0.2022 L12: 0.1475 REMARK 3 L13: 0.1011 L23: 0.0731 REMARK 3 S TENSOR REMARK 3 S11: 0.1715 S12: -0.1222 S13: -0.3953 REMARK 3 S21: 0.3901 S22: -0.2492 S23: 0.1459 REMARK 3 S31: 0.2494 S32: -0.8645 S33: -0.0041 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 48.6291 26.1310 1.0504 REMARK 3 T TENSOR REMARK 3 T11: 0.9152 T22: 0.4479 REMARK 3 T33: 0.6076 T12: 0.0695 REMARK 3 T13: -0.0362 T23: 0.0668 REMARK 3 L TENSOR REMARK 3 L11: 0.2309 L22: 0.0309 REMARK 3 L33: 0.2463 L12: -0.0613 REMARK 3 L13: 0.1566 L23: -0.0025 REMARK 3 S TENSOR REMARK 3 S11: 0.2223 S12: 0.3724 S13: 0.2348 REMARK 3 S21: 0.0171 S22: -0.4980 S23: -0.2345 REMARK 3 S31: 0.1257 S32: 0.2542 S33: 0.0004 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 48.4802 26.0716 1.8919 REMARK 3 T TENSOR REMARK 3 T11: 0.8796 T22: 0.4862 REMARK 3 T33: 0.6124 T12: 0.0325 REMARK 3 T13: -0.0431 T23: 0.0496 REMARK 3 L TENSOR REMARK 3 L11: 0.1399 L22: 0.0469 REMARK 3 L33: 0.2213 L12: 0.0024 REMARK 3 L13: 0.0067 L23: -0.0483 REMARK 3 S TENSOR REMARK 3 S11: -0.2647 S12: 0.4066 S13: 0.0998 REMARK 3 S21: 0.8945 S22: -0.1103 S23: -0.4438 REMARK 3 S31: -0.0514 S32: 0.0316 S33: -0.0333 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN E REMARK 3 ORIGIN FOR THE GROUP (A): 39.5740 19.7452 -37.5446 REMARK 3 T TENSOR REMARK 3 T11: 0.6763 T22: 0.5572 REMARK 3 T33: 0.6963 T12: 0.6323 REMARK 3 T13: -0.0450 T23: 0.0336 REMARK 3 L TENSOR REMARK 3 L11: 0.2874 L22: 1.0008 REMARK 3 L33: 0.3240 L12: 0.3491 REMARK 3 L13: 0.1774 L23: 0.1385 REMARK 3 S TENSOR REMARK 3 S11: 0.5908 S12: 0.4746 S13: 0.3806 REMARK 3 S21: 0.0403 S22: -0.8912 S23: -0.3361 REMARK 3 S31: -0.0992 S32: -0.1101 S33: -0.3141 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN F REMARK 3 ORIGIN FOR THE GROUP (A): 39.7203 20.2888 -35.9589 REMARK 3 T TENSOR REMARK 3 T11: 0.6486 T22: 0.4098 REMARK 3 T33: 0.6153 T12: 0.4087 REMARK 3 T13: -0.1512 T23: 0.0481 REMARK 3 L TENSOR REMARK 3 L11: 0.1974 L22: 0.0592 REMARK 3 L33: 0.5078 L12: 0.1404 REMARK 3 L13: -0.1179 L23: -0.1271 REMARK 3 S TENSOR REMARK 3 S11: -0.2993 S12: 0.1859 S13: 0.1424 REMARK 3 S21: 0.6490 S22: 0.1324 S23: -0.4366 REMARK 3 S31: -0.0184 S32: -0.1640 S33: -0.1069 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 148 THROUGH 149 OR REMARK 3 (RESID 150 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 151 REMARK 3 THROUGH 159 OR (RESID 160 THROUGH 161 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR REMARK 3 NAME CB OR NAME CG OR NAME CD )) OR RESID REMARK 3 162 THROUGH 166 OR (RESID 167 AND (NAME N REMARK 3 OR NAME CA OR NAME C OR NAME O OR NAME CB REMARK 3 OR NAME CG OR NAME CD )) OR RESID 168 REMARK 3 THROUGH 214 OR (RESID 215 AND (NAME N OR REMARK 3 NAME CA OR NAME CD )))) REMARK 3 SELECTION : (CHAIN B AND (RESID 148 THROUGH 184 OR REMARK 3 (RESID 185 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB OR NAME CG )) OR REMARK 3 RESID 186 THROUGH 194 OR (RESID 195 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR REMARK 3 NAME CB OR NAME CG )) OR RESID 196 REMARK 3 THROUGH 211 OR (RESID 212 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB )) REMARK 3 OR RESID 213 OR (RESID 214 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB OR REMARK 3 NAME CG )) OR RESID 215)) REMARK 3 ATOM PAIRS NUMBER : 593 REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN C AND (RESID 1 THROUGH 5 OR RESID REMARK 3 8 THROUGH 12)) REMARK 3 SELECTION : (CHAIN D AND ((RESID 1 AND (NAME C5 OR REMARK 3 NAME C4 OR NAME O4 OR NAME C3 OR NAME O3 REMARK 3 OR NAME C2 OR NAME C1 OR NAME N9 OR NAME REMARK 3 C8 OR NAME N7 OR NAME C5 OR NAME C6 OR REMARK 3 NAME O6 OR NAME N1 OR NAME C2 OR NAME N2 REMARK 3 OR NAME N3 OR NAME C4 )) OR RESID 2 REMARK 3 THROUGH 5 OR RESID 8 THROUGH 12)) REMARK 3 ATOM PAIRS NUMBER : 368 REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: (CHAIN C AND (RESID 1 THROUGH 5 OR RESID REMARK 3 8 THROUGH 12)) REMARK 3 SELECTION : (CHAIN E AND ((RESID 1 AND (NAME C5 OR REMARK 3 NAME C4 OR NAME O4 OR NAME C3 OR NAME O3 REMARK 3 OR NAME C2 OR NAME C1 OR NAME N9 OR NAME REMARK 3 C8 OR NAME N7 OR NAME C5 OR NAME C6 OR REMARK 3 NAME O6 OR NAME N1 OR NAME C2 OR NAME N2 REMARK 3 OR NAME N3 OR NAME C4 )) OR RESID 2 REMARK 3 THROUGH 5 OR RESID 8 THROUGH 12)) REMARK 3 ATOM PAIRS NUMBER : 368 REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 3 REMARK 3 REFERENCE SELECTION: (CHAIN C AND (RESID 1 THROUGH 5 OR RESID REMARK 3 8 THROUGH 12)) REMARK 3 SELECTION : (CHAIN F AND ((RESID 1 AND (NAME C5 OR REMARK 3 NAME C4 OR NAME O4 OR NAME C3 OR NAME O3 REMARK 3 OR NAME C2 OR NAME C1 OR NAME N9 OR NAME REMARK 3 C8 OR NAME N7 OR NAME C5 OR NAME C6 OR REMARK 3 NAME O6 OR NAME N1 OR NAME C2 OR NAME N2 REMARK 3 OR NAME N3 OR NAME C4 )) OR RESID 2 REMARK 3 THROUGH 5 OR RESID 8 THROUGH 12)) REMARK 3 ATOM PAIRS NUMBER : 368 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ARP/WARP WAS USED IN MAP IMPROVEMENT REMARK 3 MODE. REFMAC WAS USED AT INTERMEDIATE STAGES OF REFINEMENT. COOT REMARK 3 WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS REMARK 3 ASSESSED ON THE MOLPROBITY SERVER. REMARK 4 REMARK 4 6C2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000231957. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-13 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20266 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 40.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.86400 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: CURRENTLY UNPUBLISHED PROTEIN AND DNA MODELS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG-3350, 0.2M AMMONIUM FORMATE, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.63200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 135.26400 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 3800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, 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 350 REMARK 350 BIOMOLECULE: 2 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: 3870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F 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 142 REMARK 465 ALA A 143 REMARK 465 THR A 144 REMARK 465 GLU A 145 REMARK 465 SER A 146 REMARK 465 GLY A 147 REMARK 465 LYS A 217 REMARK 465 LEU A 218 REMARK 465 GLN A 219 REMARK 465 LYS A 220 REMARK 465 GLY B 142 REMARK 465 ALA B 143 REMARK 465 THR B 144 REMARK 465 GLU B 145 REMARK 465 SER B 146 REMARK 465 GLY B 147 REMARK 465 SER B 216 REMARK 465 LYS B 217 REMARK 465 LEU B 218 REMARK 465 GLN B 219 REMARK 465 LYS B 220 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 LYS A 148 CG CD CE NZ REMARK 470 LYS A 160 NZ REMARK 470 LYS A 161 CE NZ REMARK 470 LYS A 174 CD CE NZ REMARK 470 LYS A 185 CD CE NZ REMARK 470 ARG A 195 CD NE CZ NH1 NH2 REMARK 470 SER A 205 OG REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 MET A 214 SD CE REMARK 470 SER A 216 CA C O CB OG REMARK 470 LYS B 148 CG CD CE NZ REMARK 470 MET B 150 CG SD CE REMARK 470 LYS B 160 CE NZ REMARK 470 LYS B 161 CE NZ REMARK 470 LYS B 167 CE NZ REMARK 470 LYS B 174 CD CE NZ REMARK 470 SER B 205 OG REMARK 470 PRO B 215 C O CB CG REMARK 470 DG C 1 O5' 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 DT D 9 O3' DT D 9 C3' -0.042 REMARK 500 DG D 10 O3' DG D 10 C3' -0.040 REMARK 500 DT F 9 O3' DT F 9 C3' -0.044 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 C 3 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC F 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DA C 5 and 5CM C REMARK 800 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM C 6 and DG C REMARK 800 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DA D 5 and 5CM D REMARK 800 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM D 6 and DG D REMARK 800 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DA E 5 and 5CM E REMARK 800 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM E 6 and DG E REMARK 800 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DA F 5 and 5CM F REMARK 800 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM F 6 and DG F REMARK 800 7 DBREF 6C2E A 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C2E B 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C2E D 1 12 PDB 6C2E 6C2E 1 12 DBREF 6C2E C 1 12 PDB 6C2E 6C2E 1 12 DBREF 6C2E E 1 12 PDB 6C2E 6C2E 1 12 DBREF 6C2E F 1 12 PDB 6C2E 6C2E 1 12 SEQADV 6C2E GLY A 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2E GLY B 142 UNP Q9UBB5 EXPRESSION TAG SEQRES 1 A 79 GLY ALA THR GLU SER GLY LYS ARG MET ASP CYS PRO ALA SEQRES 2 A 79 LEU PRO PRO GLY TRP LYS LYS GLU GLU VAL ILE ARG LYS SEQRES 3 A 79 SER GLY LEU SER ALA GLY LYS SER ASP VAL TYR TYR PHE SEQRES 4 A 79 SER PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU SEQRES 5 A 79 ALA ARG TYR LEU GLY ASN THR VAL ASP LEU SER SER PHE SEQRES 6 A 79 ASP PHE ARG THR GLY LYS MET MET PRO SER LYS LEU GLN SEQRES 7 A 79 LYS SEQRES 1 B 79 GLY ALA THR GLU SER GLY LYS ARG MET ASP CYS PRO ALA SEQRES 2 B 79 LEU PRO PRO GLY TRP LYS LYS GLU GLU VAL ILE ARG LYS SEQRES 3 B 79 SER GLY LEU SER ALA GLY LYS SER ASP VAL TYR TYR PHE SEQRES 4 B 79 SER PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU SEQRES 5 B 79 ALA ARG TYR LEU GLY ASN THR VAL ASP LEU SER SER PHE SEQRES 6 B 79 ASP PHE ARG THR GLY LYS MET MET PRO SER LYS LEU GLN SEQRES 7 B 79 LYS SEQRES 1 D 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 C 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 E 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 F 12 DG DC DC DA DA 5CM DG DT DT DG DG DC HET 5CM D 6 27 HET 5CM C 6 20 HET 5CM E 6 20 HET 5CM F 6 20 HET UNX E 101 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 5CM 4(C10 H16 N3 O7 P) FORMUL 7 UNX X FORMUL 8 HOH *17(H2 O) HELIX 1 AA1 SER A 189 GLY A 198 1 10 HELIX 2 AA2 ASN A 199 VAL A 201 5 3 HELIX 3 AA3 SER B 189 GLY B 198 1 10 HELIX 4 AA4 ASN B 199 VAL B 201 5 3 SHEET 1 AA1 4 MET A 150 ASP A 151 0 SHEET 2 AA1 4 LYS A 160 ILE A 165 -1 O LYS A 161 N MET A 150 SHEET 3 AA1 4 SER A 175 PHE A 180 -1 O PHE A 180 N LYS A 160 SHEET 4 AA1 4 LYS A 186 PHE A 187 -1 O PHE A 187 N TYR A 179 SHEET 1 AA2 2 PHE A 206 ASP A 207 0 SHEET 2 AA2 2 LYS A 212 MET A 213 -1 O LYS A 212 N ASP A 207 SHEET 1 AA3 4 MET B 150 ASP B 151 0 SHEET 2 AA3 4 LYS B 160 ILE B 165 -1 O LYS B 161 N MET B 150 SHEET 3 AA3 4 SER B 175 PHE B 180 -1 O ASP B 176 N VAL B 164 SHEET 4 AA3 4 LYS B 186 PHE B 187 -1 O PHE B 187 N TYR B 179 SHEET 1 AA4 2 PHE B 206 ASP B 207 0 SHEET 2 AA4 2 LYS B 212 MET B 213 -1 O LYS B 212 N ASP B 207 LINK O3' DA D 5 P 5CM D 6 1555 1555 1.60 LINK O3'A5CM D 6 P A DG D 7 1555 1555 1.61 LINK O3'B5CM D 6 P B DG D 7 1555 1555 1.61 LINK O3' DA C 5 P 5CM C 6 1555 1555 1.59 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.61 LINK O3' DA E 5 P 5CM E 6 1555 1555 1.60 LINK O3' 5CM E 6 P DG E 7 1555 1555 1.60 LINK O3' DA F 5 P 5CM F 6 1555 1555 1.59 LINK O3' 5CM F 6 P DG F 7 1555 1555 1.61 SITE 1 AC1 13 ARG A 166 LYS A 167 SER A 168 SER A 171 SITE 2 AC1 13 ASP A 176 ARG A 188 HOH A 303 DA C 4 SITE 3 AC1 13 DG C 7 5CM D 6 DG D 7 DT D 8 SITE 4 AC1 13 DT D 9 SITE 1 AC2 12 ARG A 166 LYS A 167 SER A 168 GLY A 169 SITE 2 AC2 12 LEU A 170 SER A 171 ASP A 176 DA C 5 SITE 3 AC2 12 DT C 8 DA D 5 5CM D 6 DG D 7 SITE 1 AC3 10 ARG A 188 SER A 189 LYS A 190 PRO A 191 SITE 2 AC3 10 HOH A 305 5CM C 6 DG C 7 DT C 8 SITE 3 AC3 10 DA D 4 DG D 7 SITE 1 AC4 9 ARG A 188 SER A 189 PRO A 191 HOH A 305 SITE 2 AC4 9 DA C 5 5CM C 6 DG C 7 DA D 5 SITE 3 AC4 9 DT D 8 SITE 1 AC5 10 ARG B 188 SER B 189 LYS B 190 PRO B 191 SITE 2 AC5 10 HOH B 304 DA E 4 DG E 7 5CM F 6 SITE 3 AC5 10 DG F 7 DT F 8 SITE 1 AC6 9 ARG B 188 SER B 189 PRO B 191 HOH B 304 SITE 2 AC6 9 DA E 5 DT E 8 DA F 5 5CM F 6 SITE 3 AC6 9 DG F 7 SITE 1 AC7 12 ARG B 166 LYS B 167 SER B 168 ASP B 176 SITE 2 AC7 12 ARG B 188 HOH B 301 5CM E 6 DG E 7 SITE 3 AC7 12 DT E 8 DT E 9 DA F 4 DG F 7 SITE 1 AC8 13 ARG B 166 LYS B 167 SER B 168 GLY B 169 SITE 2 AC8 13 LEU B 170 SER B 171 ASP B 176 DA E 5 SITE 3 AC8 13 5CM E 6 DG E 7 DA F 5 DT F 8 SITE 4 AC8 13 HOH F 101 CRYST1 40.500 40.500 202.896 90.00 90.00 120.00 P 31 12 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 0.024691 0.014256 0.000000 0.00000 SCALE2 0.000000 0.028511 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004929 0.00000