HEADER DNA BINDING PROTEIN/DNA 08-JAN-18 6C2K OBSLTE 28-MAR-18 6C2K 6CNP TITLE CRYSTAL STRUCTURE OF MBD2 COMPLEX WITH METHYLATED CPG ISLAND 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: C, D, 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_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS STRUCTURAL GENOMICS CONSORTIUM, SGC, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.BIAN,W.TEMPEL,C.XU,A.K.WERNIMONT,C.BOUNTRA,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 28-MAR-18 6C2K 1 OBSLTE REVDAT 1 14-FEB-18 6C2K 0 JRNL AUTH C.BIAN,W.TEMPEL,C.XU,A.K.WERNIMONT,C.BOUNTRA,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL CRYSTAL STRUCTURE OF MBD2 COMPLEX WITH METHYLATED CPG ISLAND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 40927 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 2109 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 39.4643 - 5.1754 0.97 2566 172 0.1632 0.1804 REMARK 3 2 5.1754 - 4.1093 0.98 2590 136 0.1469 0.1672 REMARK 3 3 4.1093 - 3.5903 0.97 2644 155 0.1681 0.2085 REMARK 3 4 3.5903 - 3.2622 0.91 2411 136 0.1928 0.2137 REMARK 3 5 3.2622 - 3.0284 0.97 2585 168 0.2156 0.2299 REMARK 3 6 3.0284 - 2.8499 0.98 2589 155 0.2499 0.2872 REMARK 3 7 2.8499 - 2.7073 0.98 2591 152 0.2757 0.3531 REMARK 3 8 2.7073 - 2.5894 0.97 2653 102 0.2459 0.2486 REMARK 3 9 2.5894 - 2.4898 0.98 2604 128 0.2611 0.2763 REMARK 3 10 2.4898 - 2.4039 0.97 2600 138 0.2680 0.3471 REMARK 3 11 2.4039 - 2.3287 0.97 2661 116 0.2715 0.3161 REMARK 3 12 2.3287 - 2.2621 0.97 2549 149 0.2758 0.3451 REMARK 3 13 2.2621 - 2.2026 0.96 2576 147 0.2827 0.3502 REMARK 3 14 2.2026 - 2.1489 0.97 2576 123 0.2916 0.3790 REMARK 3 15 2.1489 - 2.1000 0.97 2623 132 0.2858 0.2630 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.77 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 : 0.010 2052 REMARK 3 ANGLE : 1.091 2972 REMARK 3 CHIRALITY : 0.061 317 REMARK 3 PLANARITY : 0.008 214 REMARK 3 DIHEDRAL : 25.982 1039 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): -6.8649 -15.1058 13.6505 REMARK 3 T TENSOR REMARK 3 T11: 0.4692 T22: 0.4437 REMARK 3 T33: 0.4671 T12: 0.0354 REMARK 3 T13: -0.0403 T23: 0.0160 REMARK 3 L TENSOR REMARK 3 L11: 1.8431 L22: 1.3599 REMARK 3 L33: 0.5436 L12: -0.3495 REMARK 3 L13: 0.4590 L23: -0.1099 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: 0.2321 S13: 0.3989 REMARK 3 S21: -0.7934 S22: -0.2541 S23: 0.5428 REMARK 3 S31: -0.4482 S32: -0.2511 S33: -0.0004 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 8.1931 -12.3098 47.2316 REMARK 3 T TENSOR REMARK 3 T11: 0.6427 T22: 0.5264 REMARK 3 T33: 0.3820 T12: -0.0286 REMARK 3 T13: 0.0097 T23: -0.0520 REMARK 3 L TENSOR REMARK 3 L11: 0.6737 L22: 2.1692 REMARK 3 L33: 1.0428 L12: -1.0699 REMARK 3 L13: -0.0222 L23: 0.7475 REMARK 3 S TENSOR REMARK 3 S11: 0.0310 S12: -0.5102 S13: 0.3245 REMARK 3 S21: 0.6271 S22: -0.0350 S23: 0.1773 REMARK 3 S31: 0.3790 S32: -0.3815 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): -5.8463 -30.9628 15.1135 REMARK 3 T TENSOR REMARK 3 T11: 0.3010 T22: 0.6182 REMARK 3 T33: 0.4810 T12: -0.0377 REMARK 3 T13: -0.0055 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.2085 L22: 0.0012 REMARK 3 L33: 0.9761 L12: -0.1232 REMARK 3 L13: -0.4076 L23: 0.2994 REMARK 3 S TENSOR REMARK 3 S11: -0.0277 S12: -0.7489 S13: -0.1554 REMARK 3 S21: -0.1374 S22: 0.0972 S23: 0.0527 REMARK 3 S31: -0.0657 S32: 0.1239 S33: -0.0005 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -5.7024 -31.4634 13.7586 REMARK 3 T TENSOR REMARK 3 T11: 0.3443 T22: 0.5566 REMARK 3 T33: 0.5572 T12: -0.0375 REMARK 3 T13: 0.0103 T23: 0.0301 REMARK 3 L TENSOR REMARK 3 L11: 1.2407 L22: 0.3667 REMARK 3 L33: 1.7426 L12: 0.5678 REMARK 3 L13: -0.4512 L23: 0.5754 REMARK 3 S TENSOR REMARK 3 S11: -0.2032 S12: 0.0738 S13: -0.5994 REMARK 3 S21: 0.1192 S22: 0.0742 S23: 0.0406 REMARK 3 S31: 0.0088 S32: -0.0250 S33: -0.0013 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN E REMARK 3 ORIGIN FOR THE GROUP (A): 11.0138 -11.1675 33.3986 REMARK 3 T TENSOR REMARK 3 T11: 0.7295 T22: 0.4081 REMARK 3 T33: 0.5633 T12: 0.0108 REMARK 3 T13: -0.0904 T23: 0.0552 REMARK 3 L TENSOR REMARK 3 L11: 1.0546 L22: 0.5121 REMARK 3 L33: 0.6037 L12: 0.8199 REMARK 3 L13: 0.3808 L23: 0.0876 REMARK 3 S TENSOR REMARK 3 S11: 0.0899 S12: 0.3082 S13: 0.2743 REMARK 3 S21: 0.6182 S22: -0.6378 S23: -0.8129 REMARK 3 S31: -0.1720 S32: -0.0705 S33: -0.1981 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN F REMARK 3 ORIGIN FOR THE GROUP (A): 9.6478 -10.9759 32.7490 REMARK 3 T TENSOR REMARK 3 T11: 0.7467 T22: 0.4231 REMARK 3 T33: 0.5043 T12: -0.0022 REMARK 3 T13: -0.0190 T23: -0.0396 REMARK 3 L TENSOR REMARK 3 L11: 1.5525 L22: 0.5169 REMARK 3 L33: 1.0017 L12: -0.5883 REMARK 3 L13: 0.0920 L23: 0.6416 REMARK 3 S TENSOR REMARK 3 S11: 0.5245 S12: 0.1402 S13: 0.0175 REMARK 3 S21: -0.2586 S22: -0.7042 S23: 0.1922 REMARK 3 S31: 0.1054 S32: 0.1556 S33: -0.0009 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PRIOR TO MOLECULAR REPLACEMENT, PROTEIN REMARK 3 COORDINATES OF THE NMR MODEL ENSEMBLE OF PDB ENTRY 2KY8 WERE REMARK 3 AVERAGED USING A PROGRAM WRITTEN BY AIPING DONG. REFMAC WAS USED REMARK 3 DURING INTERMEDIATE REFINEMENT STEPS. COOT WAS USED FOR REMARK 3 INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS ASSESSED WITH REMARK 3 MOLPROBITY. REMARK 4 REMARK 4 6C2K 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_1000231956. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-11 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 : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97947 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20704 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 39.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.97000 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: 2KY8,3QMG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG550MME, 8% PEG20000, 0.2M REMARK 280 CALCIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 2030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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: 2140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 MET A 125 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 SER A 132 REMARK 465 SER A 133 REMARK 465 GLY A 134 REMARK 465 ARG A 135 REMARK 465 GLU A 136 REMARK 465 ASN A 137 REMARK 465 LEU A 138 REMARK 465 TYR A 139 REMARK 465 PHE A 140 REMARK 465 GLN A 141 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 SER A 216 REMARK 465 LYS A 217 REMARK 465 LEU A 218 REMARK 465 GLN A 219 REMARK 465 LYS A 220 REMARK 465 MET B 125 REMARK 465 HIS B 126 REMARK 465 HIS B 127 REMARK 465 HIS B 128 REMARK 465 HIS B 129 REMARK 465 HIS B 130 REMARK 465 HIS B 131 REMARK 465 SER B 132 REMARK 465 SER B 133 REMARK 465 GLY B 134 REMARK 465 ARG B 135 REMARK 465 GLU B 136 REMARK 465 ASN B 137 REMARK 465 LEU B 138 REMARK 465 TYR B 139 REMARK 465 PHE B 140 REMARK 465 GLN B 141 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 LYS B 148 REMARK 465 ARG B 149 REMARK 465 MET B 150 REMARK 465 ASP B 151 REMARK 465 CYS B 152 REMARK 465 GLY B 211 REMARK 465 LYS B 212 REMARK 465 MET B 213 REMARK 465 MET B 214 REMARK 465 PRO B 215 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 MET A 150 SD CE REMARK 470 LYS A 160 NZ REMARK 470 LYS A 161 NZ REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 LYS A 167 CD CE NZ REMARK 470 LYS A 174 CD CE NZ REMARK 470 SER A 175 OG REMARK 470 ARG A 195 CD NE CZ NH1 NH2 REMARK 470 ARG A 209 CZ NH1 NH2 REMARK 470 LYS A 212 CD CE NZ REMARK 470 MET A 214 SD CE REMARK 470 PRO A 215 C O CB CG CD REMARK 470 PRO B 153 N CB CG CD REMARK 470 LYS B 160 CE NZ REMARK 470 GLU B 162 CD OE1 OE2 REMARK 470 LYS B 167 CD CE NZ REMARK 470 LYS B 174 CE NZ REMARK 470 SER B 175 OG REMARK 470 SER B 183 OG REMARK 470 LYS B 190 CD CE NZ REMARK 470 ASN B 199 CG OD1 ND2 REMARK 470 THR B 200 OG1 CG2 REMARK 470 ASP B 202 CG OD1 OD2 REMARK 470 SER B 205 OG REMARK 470 ARG B 209 NH1 NH2 REMARK 470 THR B 210 OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PRO A 153 UNK UNX A 309 2.14 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 DG E 8 O3' DG E 8 C3' -0.037 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 ASN B 199 43.36 -81.47 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 DC 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 DC 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 DC 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 DC 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 6C2K A 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C2K B 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C2K C 1 12 PDB 6C2K 6C2K 1 12 DBREF 6C2K D 1 12 PDB 6C2K 6C2K 1 12 DBREF 6C2K E 1 12 PDB 6C2K 6C2K 1 12 DBREF 6C2K F 1 12 PDB 6C2K 6C2K 1 12 SEQADV 6C2K MET A 125 UNP Q9UBB5 INITIATING METHIONINE SEQADV 6C2K HIS A 126 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K HIS A 127 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K HIS A 128 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K HIS A 129 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K HIS A 130 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K HIS A 131 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K SER A 132 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K SER A 133 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K GLY A 134 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K ARG A 135 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K GLU A 136 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K ASN A 137 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K LEU A 138 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K TYR A 139 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K PHE A 140 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K GLN A 141 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K GLY A 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K MET B 125 UNP Q9UBB5 INITIATING METHIONINE SEQADV 6C2K HIS B 126 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K HIS B 127 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K HIS B 128 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K HIS B 129 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K HIS B 130 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K HIS B 131 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K SER B 132 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K SER B 133 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K GLY B 134 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K ARG B 135 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K GLU B 136 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K ASN B 137 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K LEU B 138 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K TYR B 139 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K PHE B 140 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K GLN B 141 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C2K GLY B 142 UNP Q9UBB5 EXPRESSION TAG SEQRES 1 A 96 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 96 LEU TYR PHE GLN GLY ALA THR GLU SER GLY LYS ARG MET SEQRES 3 A 96 ASP CYS PRO ALA LEU PRO PRO GLY TRP LYS LYS GLU GLU SEQRES 4 A 96 VAL ILE ARG LYS SER GLY LEU SER ALA GLY LYS SER ASP SEQRES 5 A 96 VAL TYR TYR PHE SER PRO SER GLY LYS LYS PHE ARG SER SEQRES 6 A 96 LYS PRO GLN LEU ALA ARG TYR LEU GLY ASN THR VAL ASP SEQRES 7 A 96 LEU SER SER PHE ASP PHE ARG THR GLY LYS MET MET PRO SEQRES 8 A 96 SER LYS LEU GLN LYS SEQRES 1 B 96 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 B 96 LEU TYR PHE GLN GLY ALA THR GLU SER GLY LYS ARG MET SEQRES 3 B 96 ASP CYS PRO ALA LEU PRO PRO GLY TRP LYS LYS GLU GLU SEQRES 4 B 96 VAL ILE ARG LYS SER GLY LEU SER ALA GLY LYS SER ASP SEQRES 5 B 96 VAL TYR TYR PHE SER PRO SER GLY LYS LYS PHE ARG SER SEQRES 6 B 96 LYS PRO GLN LEU ALA ARG TYR LEU GLY ASN THR VAL ASP SEQRES 7 B 96 LEU SER SER PHE ASP PHE ARG THR GLY LYS MET MET PRO SEQRES 8 B 96 SER LYS LEU GLN LYS SEQRES 1 C 12 DG DC DC DA DC 5CM DG DG DT DG DG DC SEQRES 1 D 12 DG DC DC DA DC 5CM DG DG DT DG DG DC SEQRES 1 E 12 DG DC DC DA DC 5CM DG DG DT DG DG DC SEQRES 1 F 12 DG DC DC DA DC 5CM DG DG DT DG DG DC HET 5CM C 6 20 HET 5CM D 6 20 HET 5CM E 6 20 HET 5CM F 6 20 HET UNX A 301 1 HET UNX A 302 1 HET UNX A 303 1 HET UNX A 304 1 HET UNX A 305 1 HET UNX A 306 1 HET UNX A 307 1 HET UNX A 308 1 HET UNX A 309 1 HET UNX B 301 1 HET UNX D 101 1 HET UNX E 101 1 HET UNX E 102 1 HET UNX E 103 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 14(X) FORMUL 21 HOH *12(H2 O) HELIX 1 AA1 SER A 189 GLY A 198 1 10 HELIX 2 AA2 SER B 189 GLY B 198 1 10 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 TYR A 178 N GLU A 162 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 3 LYS B 160 ILE B 165 0 SHEET 2 AA3 3 SER B 175 PHE B 180 -1 O TYR B 178 N GLU B 162 SHEET 3 AA3 3 LYS B 186 PHE B 187 -1 O PHE B 187 N TYR B 179 LINK O3' DC C 5 P 5CM C 6 1555 1555 1.62 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.60 LINK O3' DC D 5 P 5CM D 6 1555 1555 1.61 LINK O3' 5CM D 6 P DG D 7 1555 1555 1.61 LINK O3' DC 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' DC F 5 P 5CM F 6 1555 1555 1.59 LINK O3' 5CM F 6 P DG F 7 1555 1555 1.60 SITE 1 AC1 10 ARG A 166 LYS A 167 SER A 168 SER A 171 SITE 2 AC1 10 ARG A 188 DA C 4 DG C 7 HOH C 101 SITE 3 AC1 10 DG D 7 DG D 8 SITE 1 AC2 13 ARG A 166 LYS A 167 SER A 168 GLY A 169 SITE 2 AC2 13 LEU A 170 SER A 171 ARG A 188 DC C 5 SITE 3 AC2 13 DG C 8 HOH C 101 DC D 5 5CM D 6 SITE 4 AC2 13 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 405 DG C 7 DG C 8 DA D 4 SITE 3 AC3 10 DG D 7 HOH D 201 SITE 1 AC4 9 ARG A 188 SER A 189 HOH A 405 DC C 5 SITE 2 AC4 9 5CM C 6 DG C 7 DG C 8 DC D 5 SITE 3 AC4 9 DG D 8 SITE 1 AC5 10 ARG B 166 LYS B 167 SER B 168 SER B 171 SITE 2 AC5 10 ASP B 176 ARG B 188 DA E 4 DG E 7 SITE 3 AC5 10 DG F 7 DG F 8 SITE 1 AC6 12 ARG B 166 LYS B 167 SER B 168 GLY B 169 SITE 2 AC6 12 LEU B 170 SER B 171 ASP B 176 DC E 5 SITE 3 AC6 12 DG E 8 DC F 5 5CM F 6 DG F 7 SITE 1 AC7 11 ARG B 188 SER B 189 LYS B 190 PRO B 191 SITE 2 AC7 11 ARG B 195 HOH B 401 DG E 7 DG E 8 SITE 3 AC7 11 DA F 4 DG F 7 HOH F 101 SITE 1 AC8 10 ARG B 188 SER B 189 PRO B 191 ARG B 195 SITE 2 AC8 10 HOH B 401 DC E 5 5CM E 6 DG E 7 SITE 3 AC8 10 DC F 5 DG F 8 CRYST1 40.960 41.320 58.670 101.57 99.46 100.54 P 1 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 0.024414 0.004544 0.005302 0.00000 SCALE2 0.000000 0.024617 0.006026 0.00000 SCALE3 0.000000 0.000000 0.017790 0.00000