HEADER TRANSCRIPTION/DNA 08-MAR-18 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 FRAGMENT: RESIDUES 143-220; COMPND 5 SYNONYM: DEMETHYLASE,DMTASE,METHYL-CPG-BINDING PROTEIN MBD2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3'); COMPND 9 CHAIN: C, D, E, F; COMPND 10 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.XU,J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 04-OCT-23 6CNP 1 LINK REVDAT 3 23-MAY-18 6CNP 1 JRNL REVDAT 2 18-APR-18 6CNP 1 JRNL REVDAT 1 28-MAR-18 6CNP 0 SPRSDE 28-MAR-18 6CNP 6C2K JRNL AUTH K.LIU,C.XU,M.LEI,A.YANG,P.LOPPNAU,T.R.HUGHES,J.MIN JRNL TITL STRUCTURAL BASIS FOR THE ABILITY OF MBD DOMAINS TO BIND JRNL TITL 2 METHYL-CG AND TG SITES IN DNA. JRNL REF J. BIOL. CHEM. V. 293 7344 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29567833 JRNL DOI 10.1074/JBC.RA118.001785 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : NULL 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.218 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 0.1569 0.1859 REMARK 3 2 5.1754 - 4.1093 0.98 2590 136 0.1440 0.1653 REMARK 3 3 4.1093 - 3.5903 0.97 2644 155 0.1627 0.2089 REMARK 3 4 3.5903 - 3.2622 0.91 2411 136 0.1851 0.2007 REMARK 3 5 3.2622 - 3.0284 0.97 2585 168 0.2061 0.2212 REMARK 3 6 3.0284 - 2.8499 0.98 2589 155 0.2358 0.2589 REMARK 3 7 2.8499 - 2.7073 0.98 2591 152 0.2591 0.3462 REMARK 3 8 2.7073 - 2.5894 0.97 2653 102 0.2341 0.2442 REMARK 3 9 2.5894 - 2.4898 0.98 2604 128 0.2541 0.2610 REMARK 3 10 2.4898 - 2.4039 0.97 2600 138 0.2535 0.3297 REMARK 3 11 2.4039 - 2.3287 0.97 2661 116 0.2569 0.3171 REMARK 3 12 2.3287 - 2.2621 0.97 2549 149 0.2602 0.3115 REMARK 3 13 2.2621 - 2.2026 0.96 2576 147 0.2706 0.3139 REMARK 3 14 2.2026 - 2.1489 0.97 2576 123 0.2828 0.3646 REMARK 3 15 2.1489 - 2.1000 0.97 2623 132 0.2762 0.2477 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.25 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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): -6.9850 -14.9644 13.5895 REMARK 3 T TENSOR REMARK 3 T11: 0.4338 T22: 0.4110 REMARK 3 T33: 0.4468 T12: 0.0300 REMARK 3 T13: -0.0550 T23: 0.0351 REMARK 3 L TENSOR REMARK 3 L11: 3.1128 L22: 3.9167 REMARK 3 L33: 1.4034 L12: -0.0595 REMARK 3 L13: 0.9301 L23: 0.2707 REMARK 3 S TENSOR REMARK 3 S11: -0.1243 S12: 0.3792 S13: 0.4865 REMARK 3 S21: -0.9275 S22: -0.2015 S23: 0.6459 REMARK 3 S31: -0.6114 S32: -0.2651 S33: 0.2232 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 8.2251 -12.3251 47.3323 REMARK 3 T TENSOR REMARK 3 T11: 0.6498 T22: 0.5171 REMARK 3 T33: 0.3852 T12: -0.0461 REMARK 3 T13: -0.0080 T23: -0.0559 REMARK 3 L TENSOR REMARK 3 L11: 0.8172 L22: 2.8888 REMARK 3 L33: 1.8160 L12: -1.0945 REMARK 3 L13: -0.0912 L23: 0.7736 REMARK 3 S TENSOR REMARK 3 S11: 0.1387 S12: -0.7139 S13: 0.1742 REMARK 3 S21: 0.8860 S22: -0.0567 S23: 0.1135 REMARK 3 S31: 0.5603 S32: -0.3634 S33: -0.1203 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): -5.8193 -30.8832 15.0722 REMARK 3 T TENSOR REMARK 3 T11: 0.3285 T22: 0.6060 REMARK 3 T33: 0.4810 T12: -0.0451 REMARK 3 T13: -0.0083 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 3.1008 L22: 1.0732 REMARK 3 L33: 2.6678 L12: -0.7214 REMARK 3 L13: -0.2274 L23: 0.4443 REMARK 3 S TENSOR REMARK 3 S11: -0.0435 S12: -0.7379 S13: -0.1887 REMARK 3 S21: -0.1377 S22: 0.1296 S23: 0.0140 REMARK 3 S31: -0.0440 S32: 0.1711 S33: 0.0290 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -5.6665 -31.3804 13.7199 REMARK 3 T TENSOR REMARK 3 T11: 0.3504 T22: 0.5263 REMARK 3 T33: 0.5702 T12: -0.0341 REMARK 3 T13: 0.0030 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 3.4529 L22: 0.7037 REMARK 3 L33: 2.2768 L12: 0.6502 REMARK 3 L13: -0.4480 L23: 0.4805 REMARK 3 S TENSOR REMARK 3 S11: -0.0972 S12: 0.2274 S13: -0.5896 REMARK 3 S21: 0.0036 S22: 0.0212 S23: -0.0385 REMARK 3 S31: 0.0917 S32: 0.0287 S33: 0.1077 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN E REMARK 3 ORIGIN FOR THE GROUP (A): 11.0376 -11.0817 33.3484 REMARK 3 T TENSOR REMARK 3 T11: 0.7162 T22: 0.4358 REMARK 3 T33: 0.5336 T12: 0.0072 REMARK 3 T13: -0.1068 T23: 0.0513 REMARK 3 L TENSOR REMARK 3 L11: 2.2245 L22: 4.4768 REMARK 3 L33: 2.0068 L12: 1.1137 REMARK 3 L13: 0.5922 L23: -0.1070 REMARK 3 S TENSOR REMARK 3 S11: 0.1065 S12: 0.2189 S13: 0.3720 REMARK 3 S21: 0.7312 S22: -0.6460 S23: -0.8608 REMARK 3 S31: -0.2195 S32: -0.0773 S33: 0.5033 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN F REMARK 3 ORIGIN FOR THE GROUP (A): 9.6715 -10.8887 32.7005 REMARK 3 T TENSOR REMARK 3 T11: 0.7163 T22: 0.4237 REMARK 3 T33: 0.4894 T12: -0.0126 REMARK 3 T13: -0.0238 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 2.6358 L22: 4.7476 REMARK 3 L33: 1.8724 L12: -1.5504 REMARK 3 L13: 0.0168 L23: 1.6649 REMARK 3 S TENSOR REMARK 3 S11: 0.5189 S12: 0.1712 S13: 0.0261 REMARK 3 S21: -0.4307 S22: -0.6190 S23: 0.3591 REMARK 3 S31: 0.0342 S32: 0.0845 S33: 0.1570 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 6CNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000233101. 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: PDB ENTRIES 2KY8, 3QMG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 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: 3800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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: 3890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7120 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 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 LYS A 212 CD CE NZ REMARK 470 MET A 214 SD CE REMARK 470 LYS B 160 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 LEU B 203 O 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 HOH A 414 O HOH A 416 2.15 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 47.30 -89.14 REMARK 500 THR B 200 28.64 -144.18 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 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 153 O REMARK 620 2 LEU A 155 O 85.7 REMARK 620 3 HOH A 414 O 75.9 156.2 REMARK 620 4 HOH A 416 O 80.6 141.8 50.0 REMARK 620 5 DT D 9 OP1 68.7 17.0 141.5 133.5 REMARK 620 6 HOH D 105 O 106.4 79.5 119.9 70.7 85.1 REMARK 620 7 HOH D 107 O 96.3 78.3 88.7 138.3 80.9 146.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 301 DBREF 6CNP A 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6CNP B 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6CNP C 1 12 PDB 6CNP 6CNP 1 12 DBREF 6CNP D 1 12 PDB 6CNP 6CNP 1 12 DBREF 6CNP E 1 12 PDB 6CNP 6CNP 1 12 DBREF 6CNP F 1 12 PDB 6CNP 6CNP 1 12 SEQADV 6CNP MET A 125 UNP Q9UBB5 INITIATING METHIONINE SEQADV 6CNP HIS A 126 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP HIS A 127 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP HIS A 128 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP HIS A 129 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP HIS A 130 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP HIS A 131 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP SER A 132 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP SER A 133 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP GLY A 134 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP ARG A 135 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP GLU A 136 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP ASN A 137 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP LEU A 138 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP TYR A 139 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP PHE A 140 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP GLN A 141 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP GLY A 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP MET B 125 UNP Q9UBB5 INITIATING METHIONINE SEQADV 6CNP HIS B 126 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP HIS B 127 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP HIS B 128 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP HIS B 129 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP HIS B 130 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP HIS B 131 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP SER B 132 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP SER B 133 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP GLY B 134 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP ARG B 135 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP GLU B 136 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP ASN B 137 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP LEU B 138 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP TYR B 139 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP PHE B 140 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP GLN B 141 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNP 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 CA 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 B 301 1 HET UNX E 101 1 HET UNX E 102 1 HET UNX F 101 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 5CM 4(C10 H16 N3 O7 P) FORMUL 7 CA CA 2+ FORMUL 8 UNX 11(X) FORMUL 19 HOH *34(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 1.61 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 LINK O PRO A 153 CA CA A 301 1555 1555 2.26 LINK O LEU A 155 CA CA A 301 1555 1555 2.41 LINK CA CA A 301 O HOH A 414 1555 1555 2.56 LINK CA CA A 301 O HOH A 416 1555 1555 2.51 LINK CA CA A 301 OP1 DT D 9 1545 1555 2.36 LINK CA CA A 301 O HOH D 105 1555 1565 2.24 LINK CA CA A 301 O HOH D 107 1555 1565 2.60 SITE 1 AC1 7 PRO A 153 LEU A 155 HOH A 414 HOH A 416 SITE 2 AC1 7 DT D 9 HOH D 105 HOH D 107 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