PDB Short entry for 6C1V HEADER DNA BINDING PROTEIN/DNA 05-JAN-18 6C1V TITLE MBD2 IN COMPLEX WITH DOUBLE-STRANDED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 2; COMPND 3 CHAIN: A, B, E, F; 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, G; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 12-MER DNA; COMPND 12 CHAIN: D, H; 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 6C1V 1 REMARK REVDAT 4 13-MAR-24 6C1V 1 REMARK REVDAT 3 23-MAY-18 6C1V 1 JRNL REVDAT 2 18-APR-18 6C1V 1 JRNL REVDAT 1 14-FEB-18 6C1V 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. 2.30 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 22079 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.600 REMARK 3 FREE R VALUE TEST SET COUNT : 821 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1738 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 1 REMARK 3 BIN FREE R VALUE : 0.1100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2024 REMARK 3 NUCLEIC ACID ATOMS : 972 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.70000 REMARK 3 B22 (A**2) : 0.58000 REMARK 3 B33 (A**2) : 0.34000 REMARK 3 B12 (A**2) : -0.48000 REMARK 3 B13 (A**2) : 0.31000 REMARK 3 B23 (A**2) : 0.04000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.306 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.235 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.188 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.487 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3162 ; 0.015 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 2398 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4462 ; 1.786 ; 1.672 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5554 ; 1.230 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 268 ; 6.780 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;30.659 ;21.282 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 329 ;14.439 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;20.108 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 426 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2905 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 717 ; 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): 1078 ; 1.365 ; 2.903 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1075 ; 1.357 ; 2.899 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1342 ; 2.161 ; 4.343 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 : 8 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): -28.0331 16.3941 -25.1840 REMARK 3 T TENSOR REMARK 3 T11: 0.1832 T22: 0.2958 REMARK 3 T33: 0.0977 T12: -0.0835 REMARK 3 T13: 0.0152 T23: -0.0533 REMARK 3 L TENSOR REMARK 3 L11: 2.7819 L22: 3.2849 REMARK 3 L33: 6.4315 L12: -1.7094 REMARK 3 L13: -0.2781 L23: 1.8401 REMARK 3 S TENSOR REMARK 3 S11: -0.0185 S12: -0.3048 S13: 0.0401 REMARK 3 S21: 0.3543 S22: 0.1616 S23: -0.2959 REMARK 3 S31: -0.1784 S32: 0.3234 S33: -0.1431 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 147 B 214 REMARK 3 ORIGIN FOR THE GROUP (A): -45.7542 7.4734 -54.5380 REMARK 3 T TENSOR REMARK 3 T11: 0.4152 T22: 0.3319 REMARK 3 T33: 0.0756 T12: -0.0685 REMARK 3 T13: -0.0646 T23: -0.0449 REMARK 3 L TENSOR REMARK 3 L11: 3.9040 L22: 2.2721 REMARK 3 L33: 7.6943 L12: -0.8871 REMARK 3 L13: -3.8410 L23: -0.9780 REMARK 3 S TENSOR REMARK 3 S11: 0.1010 S12: 0.7029 S13: -0.0053 REMARK 3 S21: -0.7440 S22: -0.1199 S23: 0.1925 REMARK 3 S31: 0.0388 S32: -0.5785 S33: 0.0188 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): -34.9881 17.1824 -39.7780 REMARK 3 T TENSOR REMARK 3 T11: 0.0836 T22: 0.1073 REMARK 3 T33: 0.0666 T12: -0.0338 REMARK 3 T13: 0.0327 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 4.0696 L22: 7.5136 REMARK 3 L33: 2.6519 L12: 4.4098 REMARK 3 L13: 0.1737 L23: 2.0075 REMARK 3 S TENSOR REMARK 3 S11: -0.1137 S12: -0.0013 S13: 0.2188 REMARK 3 S21: -0.5063 S22: 0.1228 S23: -0.0491 REMARK 3 S31: -0.2106 S32: 0.0013 S33: -0.0091 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 1 D 12 REMARK 3 ORIGIN FOR THE GROUP (A): -33.6925 17.0309 -40.5977 REMARK 3 T TENSOR REMARK 3 T11: 0.1151 T22: 0.0635 REMARK 3 T33: 0.0945 T12: -0.0326 REMARK 3 T13: 0.0073 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 5.3194 L22: 9.5890 REMARK 3 L33: 2.2356 L12: 5.0339 REMARK 3 L13: 0.1482 L23: 1.0933 REMARK 3 S TENSOR REMARK 3 S11: 0.1684 S12: -0.1736 S13: 0.1191 REMARK 3 S21: -0.0537 S22: -0.1472 S23: -0.4886 REMARK 3 S31: -0.1193 S32: -0.0143 S33: -0.0212 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 148 E 215 REMARK 3 ORIGIN FOR THE GROUP (A): -46.6790 14.7521 -5.5113 REMARK 3 T TENSOR REMARK 3 T11: 0.1483 T22: 0.2663 REMARK 3 T33: 0.1194 T12: 0.1311 REMARK 3 T13: 0.0129 T23: -0.0478 REMARK 3 L TENSOR REMARK 3 L11: 3.2222 L22: 3.5151 REMARK 3 L33: 6.3837 L12: 2.0949 REMARK 3 L13: 1.3741 L23: 1.5081 REMARK 3 S TENSOR REMARK 3 S11: -0.0739 S12: 0.4070 S13: -0.0841 REMARK 3 S21: -0.3608 S22: 0.2242 S23: -0.2832 REMARK 3 S31: 0.1613 S32: 0.2632 S33: -0.1503 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 148 F 215 REMARK 3 ORIGIN FOR THE GROUP (A): -64.6416 23.5196 23.9552 REMARK 3 T TENSOR REMARK 3 T11: 0.3260 T22: 0.2338 REMARK 3 T33: 0.0646 T12: 0.0264 REMARK 3 T13: 0.0369 T23: -0.0265 REMARK 3 L TENSOR REMARK 3 L11: 2.9375 L22: 2.9904 REMARK 3 L33: 6.6368 L12: 0.2868 REMARK 3 L13: 0.8090 L23: -0.7861 REMARK 3 S TENSOR REMARK 3 S11: 0.1079 S12: -0.6228 S13: -0.0316 REMARK 3 S21: 0.8571 S22: -0.1334 S23: 0.0681 REMARK 3 S31: -0.1685 S32: -0.2287 S33: 0.0255 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : G 1 G 12 REMARK 3 ORIGIN FOR THE GROUP (A): -53.3202 13.7600 9.0937 REMARK 3 T TENSOR REMARK 3 T11: 0.2293 T22: 0.0708 REMARK 3 T33: 0.0905 T12: 0.1058 REMARK 3 T13: -0.0577 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 4.2394 L22: 6.6927 REMARK 3 L33: 3.5131 L12: -4.2440 REMARK 3 L13: -0.4757 L23: 3.2384 REMARK 3 S TENSOR REMARK 3 S11: -0.1434 S12: -0.0033 S13: -0.2234 REMARK 3 S21: 0.6303 S22: 0.2067 S23: 0.0663 REMARK 3 S31: 0.3517 S32: 0.1291 S33: -0.0633 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 12 REMARK 3 ORIGIN FOR THE GROUP (A): -52.1080 13.9855 9.8699 REMARK 3 T TENSOR REMARK 3 T11: 0.1114 T22: 0.0416 REMARK 3 T33: 0.1129 T12: 0.0605 REMARK 3 T13: 0.0151 T23: 0.0214 REMARK 3 L TENSOR REMARK 3 L11: 5.1224 L22: 8.6126 REMARK 3 L33: 2.0870 L12: -4.5310 REMARK 3 L13: 0.3755 L23: 0.1376 REMARK 3 S TENSOR REMARK 3 S11: 0.2114 S12: 0.2075 S13: -0.2120 REMARK 3 S21: 0.0508 S22: -0.1743 S23: -0.3675 REMARK 3 S31: 0.1930 S32: 0.0249 S33: -0.0370 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6C1V 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_1000230208. 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 : 6.5 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 : 34483 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.76000 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: RIGID BODY REFINEMENT (REFMAC5/DIMPLE) OF A REMARK 200 CURRENTLY UNPUBLISHED, ISOMORPHOUS STRUCTURE OF A SIMILAR MBD2- REMARK 200 DNA COMPLEX AGAINST CURRENT DATA. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG-3350, 0.1 M BIS-TRIS, PH 6.5, REMARK 280 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: TETRAMERIC 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H 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 B 142 REMARK 465 ALA B 143 REMARK 465 THR B 144 REMARK 465 GLU B 145 REMARK 465 SER B 146 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 465 GLY E 142 REMARK 465 ALA E 143 REMARK 465 THR E 144 REMARK 465 GLU E 145 REMARK 465 SER E 146 REMARK 465 GLY E 147 REMARK 465 SER E 216 REMARK 465 LYS E 217 REMARK 465 LEU E 218 REMARK 465 GLN E 219 REMARK 465 LYS E 220 REMARK 465 GLY F 142 REMARK 465 ALA F 143 REMARK 465 THR F 144 REMARK 465 GLU F 145 REMARK 465 SER F 146 REMARK 465 GLY F 147 REMARK 465 SER F 216 REMARK 465 LYS F 217 REMARK 465 LEU F 218 REMARK 465 GLN F 219 REMARK 465 LYS F 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 NZ REMARK 470 LYS A 167 CD CE NZ REMARK 470 LEU A 170 CG CD1 CD2 REMARK 470 SER A 171 OG REMARK 470 LYS A 174 CE NZ REMARK 470 SER A 183 OG REMARK 470 LYS A 185 CG CD CE NZ REMARK 470 LYS A 212 CE NZ REMARK 470 PRO A 215 CB CG CD REMARK 470 LYS B 148 CG CD CE NZ REMARK 470 MET B 150 CG SD CE REMARK 470 ASP B 151 CG OD1 OD2 REMARK 470 PRO B 153 CB CG CD REMARK 470 PRO B 157 CB CG CD REMARK 470 LYS B 160 CD CE NZ REMARK 470 LYS B 161 NZ REMARK 470 LYS B 167 CD CE NZ REMARK 470 SER B 183 OG REMARK 470 LYS B 185 CG CD CE NZ REMARK 470 LYS B 186 NZ REMARK 470 ASN B 199 OD1 ND2 REMARK 470 SER B 205 OG REMARK 470 LYS B 212 CD CE NZ REMARK 470 MET B 214 C O CB CG SD CE REMARK 470 LYS E 148 CG CD CE NZ REMARK 470 LYS E 160 NZ REMARK 470 LYS E 161 NZ REMARK 470 LYS E 167 CD CE NZ REMARK 470 LEU E 170 CG CD1 CD2 REMARK 470 SER E 171 OG REMARK 470 LYS E 174 CE NZ REMARK 470 SER E 183 OG REMARK 470 LYS E 185 NZ REMARK 470 ARG E 209 NH1 NH2 REMARK 470 LYS E 212 CE NZ REMARK 470 PRO E 215 C O CB CG CD REMARK 470 LYS F 148 CG CD CE NZ REMARK 470 MET F 150 CG SD CE REMARK 470 ASP F 151 CG OD1 OD2 REMARK 470 LYS F 160 CE NZ REMARK 470 LYS F 161 NZ REMARK 470 SER F 183 OG REMARK 470 LYS F 185 CG CD CE NZ REMARK 470 LYS F 186 CE NZ REMARK 470 ARG F 195 CG CD NE CZ NH1 NH2 REMARK 470 ASN F 199 CG OD1 ND2 REMARK 470 THR F 200 OG1 CG2 REMARK 470 LYS F 212 NZ REMARK 470 PRO F 215 C O CB CG CD 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 ARG A 195 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 DT C 8 O5' - P - OP1 ANGL. DEV. = -6.8 DEGREES REMARK 500 DA H 5 O5' - P - OP2 ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA B 172 124.13 -31.91 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 D 9 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 6C1V A 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1V B 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1V C 1 12 PDB 6C1V 6C1V 1 12 DBREF 6C1V D 1 12 PDB 6C1V 6C1V 1 12 DBREF 6C1V E 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1V F 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1V G 1 12 PDB 6C1V 6C1V 1 12 DBREF 6C1V H 1 12 PDB 6C1V 6C1V 1 12 SEQADV 6C1V GLY A 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C1V GLY B 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C1V GLY E 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C1V GLY F 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 C 12 DC DG DG DA DG DT DG DT DA DG DG DC SEQRES 1 D 12 DG DC DC DT DA DC DA DC DT DC DC DG SEQRES 1 E 79 GLY ALA THR GLU SER GLY LYS ARG MET ASP CYS PRO ALA SEQRES 2 E 79 LEU PRO PRO GLY TRP LYS LYS GLU GLU VAL ILE ARG LYS SEQRES 3 E 79 SER GLY LEU SER ALA GLY LYS SER ASP VAL TYR TYR PHE SEQRES 4 E 79 SER PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU SEQRES 5 E 79 ALA ARG TYR LEU GLY ASN THR VAL ASP LEU SER SER PHE SEQRES 6 E 79 ASP PHE ARG THR GLY LYS MET MET PRO SER LYS LEU GLN SEQRES 7 E 79 LYS SEQRES 1 F 79 GLY ALA THR GLU SER GLY LYS ARG MET ASP CYS PRO ALA SEQRES 2 F 79 LEU PRO PRO GLY TRP LYS LYS GLU GLU VAL ILE ARG LYS SEQRES 3 F 79 SER GLY LEU SER ALA GLY LYS SER ASP VAL TYR TYR PHE SEQRES 4 F 79 SER PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU SEQRES 5 F 79 ALA ARG TYR LEU GLY ASN THR VAL ASP LEU SER SER PHE SEQRES 6 F 79 ASP PHE ARG THR GLY LYS MET MET PRO SER LYS LEU GLN SEQRES 7 F 79 LYS SEQRES 1 G 12 DC DG DG DA DG DT DG DT DA DG DG DC SEQRES 1 H 12 DG DC DC DT DA DC DA DC DT DC DC DG 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 B 302 1 HET UNX B 303 1 HET UNX B 304 1 HET UNX B 305 1 HET UNX B 306 1 HET UNX C 101 1 HET UNX C 102 1 HET UNX C 103 1 HET UNX C 104 1 HET UNX D 101 1 HET UNX E 301 1 HET UNX E 302 1 HET UNX E 303 1 HET UNX E 304 1 HET UNX E 305 1 HET UNX E 306 1 HET UNX E 307 1 HET UNX F 301 1 HET UNX F 302 1 HET UNX F 303 1 HET UNX F 304 1 HET UNX G 101 1 HET UNX G 102 1 HET UNX G 103 1 HET UNX G 104 1 HET UNX H 101 1 HETNAM UNX UNKNOWN ATOM OR ION FORMUL 9 UNX 36(X) FORMUL 45 HOH *29(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 HELIX 5 AA5 SER E 189 GLY E 198 1 10 HELIX 6 AA6 ASN E 199 VAL E 201 5 3 HELIX 7 AA7 SER F 189 GLY F 198 1 10 HELIX 8 AA8 ASN F 199 VAL F 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 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 TYR B 178 N GLU B 162 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 SHEET 1 AA5 4 MET E 150 ASP E 151 0 SHEET 2 AA5 4 LYS E 160 ILE E 165 -1 O LYS E 161 N MET E 150 SHEET 3 AA5 4 SER E 175 PHE E 180 -1 O TYR E 178 N GLU E 162 SHEET 4 AA5 4 LYS E 186 PHE E 187 -1 O PHE E 187 N TYR E 179 SHEET 1 AA6 2 PHE E 206 ASP E 207 0 SHEET 2 AA6 2 LYS E 212 MET E 213 -1 O LYS E 212 N ASP E 207 SHEET 1 AA7 4 MET F 150 ASP F 151 0 SHEET 2 AA7 4 LYS F 160 ILE F 165 -1 O LYS F 161 N MET F 150 SHEET 3 AA7 4 SER F 175 PHE F 180 -1 O TYR F 178 N GLU F 162 SHEET 4 AA7 4 LYS F 186 PHE F 187 -1 O PHE F 187 N TYR F 179 SHEET 1 AA8 2 PHE F 206 ASP F 207 0 SHEET 2 AA8 2 LYS F 212 MET F 213 -1 O LYS F 212 N ASP F 207 CRYST1 37.013 40.198 105.158 84.50 85.48 62.71 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 0.027018 -0.013937 -0.001200 0.00000 SCALE2 0.000000 0.027992 -0.001892 0.00000 SCALE3 0.000000 0.000000 0.009561 0.00000