PDB Short entry for 6C1T HEADER DNA BINDING PROTEIN/DNA 05-JAN-18 6C1T TITLE MBD2 IN COMPLEX WITH A PARTIALLY METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 2; COMPND 3 CHAIN: A, D; 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: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 12-MER DNA; COMPND 12 CHAIN: C; COMPND 13 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-RIL; 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 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630 KEYWDS MBD, DNA-BINDING, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.LEI,W.TEMPEL,C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,J.MIN,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (SGC) REVDAT 5 03-APR-24 6C1T 1 REMARK REVDAT 4 13-MAR-24 6C1T 1 REMARK REVDAT 3 23-MAY-18 6C1T 1 JRNL REVDAT 2 18-APR-18 6C1T 1 JRNL REVDAT 1 14-FEB-18 6C1T 0 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. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 21271 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1095 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1428 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 996 REMARK 3 NUCLEIC ACID ATOMS : 487 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.129 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.995 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1576 ; 0.014 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 1195 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2229 ; 1.758 ; 1.701 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2771 ; 1.182 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 131 ; 6.071 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 38 ;29.368 ;21.579 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 157 ;11.697 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;20.662 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 216 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1434 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 346 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 531 ; 1.375 ; 2.957 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 530 ; 1.376 ; 2.953 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 661 ; 2.027 ; 4.418 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 148 A 215 REMARK 3 ORIGIN FOR THE GROUP (A): -15.1745 26.9201 108.8401 REMARK 3 T TENSOR REMARK 3 T11: 0.1818 T22: 0.0948 REMARK 3 T33: 0.0158 T12: -0.0658 REMARK 3 T13: -0.0001 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 2.8517 L22: 3.7358 REMARK 3 L33: 6.3125 L12: -0.9724 REMARK 3 L13: 1.3119 L23: -1.2599 REMARK 3 S TENSOR REMARK 3 S11: 0.0445 S12: 0.0091 S13: -0.2085 REMARK 3 S21: -0.2683 S22: 0.0849 S23: 0.0972 REMARK 3 S31: 0.3120 S32: -0.0897 S33: -0.1294 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 12 REMARK 3 ORIGIN FOR THE GROUP (A): -15.9714 32.1378 124.1032 REMARK 3 T TENSOR REMARK 3 T11: 0.0940 T22: 0.1452 REMARK 3 T33: 0.0586 T12: -0.0233 REMARK 3 T13: 0.0348 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 8.0348 L22: 3.9760 REMARK 3 L33: 1.8834 L12: 4.0273 REMARK 3 L13: 0.9462 L23: -0.3218 REMARK 3 S TENSOR REMARK 3 S11: -0.1763 S12: -0.1470 S13: -0.3687 REMARK 3 S21: -0.1475 S22: 0.0971 S23: -0.0461 REMARK 3 S31: 0.0775 S32: -0.1042 S33: 0.0792 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 12 REMARK 3 ORIGIN FOR THE GROUP (A): -16.1925 33.4383 123.3795 REMARK 3 T TENSOR REMARK 3 T11: 0.1319 T22: 0.1569 REMARK 3 T33: 0.0091 T12: -0.0570 REMARK 3 T13: 0.0013 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 6.7615 L22: 3.8020 REMARK 3 L33: 0.7873 L12: 3.9007 REMARK 3 L13: 0.8079 L23: -0.1614 REMARK 3 S TENSOR REMARK 3 S11: -0.0883 S12: -0.1743 S13: 0.2003 REMARK 3 S21: -0.0173 S22: 0.0538 S23: 0.1574 REMARK 3 S31: -0.0071 S32: -0.1591 S33: 0.0345 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 149 D 214 REMARK 3 ORIGIN FOR THE GROUP (A): -6.0204 43.8811 138.4985 REMARK 3 T TENSOR REMARK 3 T11: 0.2923 T22: 0.5024 REMARK 3 T33: 0.1006 T12: -0.0733 REMARK 3 T13: -0.0502 T23: -0.0461 REMARK 3 L TENSOR REMARK 3 L11: 2.2468 L22: 5.3269 REMARK 3 L33: 7.1232 L12: 0.0718 REMARK 3 L13: -1.6750 L23: -2.9222 REMARK 3 S TENSOR REMARK 3 S11: -0.0129 S12: -0.8720 S13: 0.2677 REMARK 3 S21: 0.8714 S22: -0.0727 S23: -0.0660 REMARK 3 S31: -0.3416 S32: 0.2516 S33: 0.0857 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE IDENTITY OF THE 'SULFATE' NEAR SER REMARK 3 -183 IS UNCLEAR. SIMILAR DENSITY WAS ALSO OBSERVED IN ANOTHER REMARK 3 MBD2-DNA COMPLEX CRYSTAL WHERE THE CRYSTALLIZATION BUFFER DID REMARK 3 NOT INCLUDE SULFATE. REMARK 4 REMARK 4 6C1T 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_1000230207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22367 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 49.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 1.24400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 MODEL OF MBD2-DNA COMPLEX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG-3350, 0.1 M BIS-TRIS, 0.15 M REMARK 280 AMMONIUM SULFATE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.73650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.46650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.73650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.46650 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 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 GLY D 142 REMARK 465 ALA D 143 REMARK 465 THR D 144 REMARK 465 GLU D 145 REMARK 465 SER D 146 REMARK 465 GLY D 147 REMARK 465 LYS D 148 REMARK 465 PRO D 215 REMARK 465 SER D 216 REMARK 465 LYS D 217 REMARK 465 LEU D 218 REMARK 465 GLN D 219 REMARK 465 LYS D 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 161 NZ REMARK 470 LYS A 167 CD CE NZ REMARK 470 SER A 171 OG REMARK 470 LYS A 174 CD CE NZ 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 PRO A 215 CA C O CB CG CD REMARK 470 MET D 150 CG SD CE REMARK 470 ASP D 151 CG OD1 OD2 REMARK 470 LYS D 160 CG CD CE NZ REMARK 470 LYS D 167 CD CE NZ REMARK 470 LYS D 174 CE NZ REMARK 470 SER D 183 OG REMARK 470 LYS D 185 CG CD CE NZ REMARK 470 LYS D 186 CG CD CE NZ REMARK 470 ARG D 195 CG CD NE CZ NH1 NH2 REMARK 470 ASN D 199 CG OD1 ND2 REMARK 470 THR D 200 OG1 CG2 REMARK 470 LYS D 212 CD CE NZ 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 DA B 5 O5' - P - OP2 ANGL. DEV. = -9.8 DEGREES REMARK 500 DC B 8 O5' - P - OP2 ANGL. DEV. = -5.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DT B 9 0.07 SIDE CHAIN 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 residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 106 DBREF 6C1T A 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1T B 1 12 PDB 6C1T 6C1T 1 12 DBREF 6C1T C 1 12 PDB 6C1T 6C1T 1 12 DBREF 6C1T D 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 SEQADV 6C1T GLY A 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C1T GLY D 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 12 DG DC DC DT DA 5CM DA DC DT DC DC DG SEQRES 1 C 12 DC DG DG DA DG DT DG DT DA DG DG DC SEQRES 1 D 79 GLY ALA THR GLU SER GLY LYS ARG MET ASP CYS PRO ALA SEQRES 2 D 79 LEU PRO PRO GLY TRP LYS LYS GLU GLU VAL ILE ARG LYS SEQRES 3 D 79 SER GLY LEU SER ALA GLY LYS SER ASP VAL TYR TYR PHE SEQRES 4 D 79 SER PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU SEQRES 5 D 79 ALA ARG TYR LEU GLY ASN THR VAL ASP LEU SER SER PHE SEQRES 6 D 79 ASP PHE ARG THR GLY LYS MET MET PRO SER LYS LEU GLN SEQRES 7 D 79 LYS HET 5CM B 6 20 HET SO4 A 301 5 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 A 310 1 HET UNX A 311 1 HET UNX A 312 1 HET UNX A 313 1 HET UNX A 314 1 HET UNX B 101 1 HET UNX B 102 1 HET UNX B 103 1 HET UNX C 101 1 HET UNX C 102 1 HET UNX C 103 1 HET UNX C 104 1 HET UNX C 105 1 HET GOL C 106 6 HET UNX D 301 1 HET UNX D 302 1 HET UNX D 303 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SO4 SULFATE ION HETNAM UNX UNKNOWN ATOM OR ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 5 SO4 O4 S 2- FORMUL 6 UNX 24(X) FORMUL 27 GOL C3 H8 O3 FORMUL 31 HOH *41(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 D 189 GLY D 198 1 10 HELIX 4 AA4 ASN D 199 VAL D 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 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 4 MET D 150 ASP D 151 0 SHEET 2 AA3 4 LYS D 160 ILE D 165 -1 O LYS D 161 N MET D 150 SHEET 3 AA3 4 SER D 175 PHE D 180 -1 O TYR D 178 N GLU D 162 SHEET 4 AA3 4 LYS D 186 PHE D 187 -1 O PHE D 187 N TYR D 179 SHEET 1 AA4 2 PHE D 206 ASP D 207 0 SHEET 2 AA4 2 LYS D 212 MET D 213 -1 O LYS D 212 N ASP D 207 LINK O3' DA B 5 P 5CM B 6 1555 1555 1.58 LINK O3' 5CM B 6 P DA B 7 1555 1555 1.59 SITE 1 AC1 5 SER A 181 PRO A 182 SER A 183 LYS A 185 SITE 2 AC1 5 TYR A 196 SITE 1 AC2 8 DC C 1 DG C 11 HOH C 201 HOH C 204 SITE 2 AC2 8 ILE D 165 ARG D 166 LYS D 167 HOH D 402 CRYST1 71.473 36.933 104.076 90.00 108.25 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013991 0.000000 0.004613 0.00000 SCALE2 0.000000 0.027076 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010117 0.00000