PDB Short entry for 6C1A HEADER DNA BINDING PROTEIN/DNA 04-JAN-18 6C1A TITLE MBD2 IN COMPLEX WITH METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 2; COMPND 3 CHAIN: A, B, E, F; COMPND 4 SYNONYM: DEMETHYLASE,DMTASE,METHYL-CPG-BINDING PROTEIN MBD2; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA STRAND 1; COMPND 8 CHAIN: C, G; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: COMPLEMENT TO DNA STRAND 1; 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-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 OTHER_DETAILS: SYNTHETIC; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 OTHER_DETAILS: SYNTHETIC KEYWDS DNA METHYLATION, DNA BINDING, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.LIU,C.XU,W.TEMPEL,C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,J.MIN, AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 5 03-APR-24 6C1A 1 REMARK REVDAT 4 13-MAR-24 6C1A 1 REMARK REVDAT 3 23-MAY-18 6C1A 1 JRNL REVDAT 2 18-APR-18 6C1A 1 JRNL REVDAT 1 14-FEB-18 6C1A 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. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 30448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS (SFTOOLS) REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1224 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2264 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3200 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2037 REMARK 3 NUCLEIC ACID ATOMS : 974 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.71000 REMARK 3 B33 (A**2) : 1.08000 REMARK 3 B12 (A**2) : -0.02000 REMARK 3 B13 (A**2) : 0.20000 REMARK 3 B23 (A**2) : 0.11000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.207 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.181 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.157 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.006 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 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): 3209 ; 0.013 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 2468 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4528 ; 1.517 ; 1.700 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5719 ; 1.138 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 271 ; 5.713 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;27.573 ;21.059 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 349 ;12.377 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;19.720 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 432 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2937 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 713 ; 0.001 ; 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): 1080 ; 1.045 ; 2.125 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1077 ; 1.039 ; 2.121 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1346 ; 1.688 ; 3.175 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 147 A 214 REMARK 3 ORIGIN FOR THE GROUP (A): -27.6912 15.6961 -25.5338 REMARK 3 T TENSOR REMARK 3 T11: 0.0708 T22: 0.1341 REMARK 3 T33: 0.0283 T12: -0.0634 REMARK 3 T13: -0.0115 T23: -0.0285 REMARK 3 L TENSOR REMARK 3 L11: 3.5253 L22: 2.0427 REMARK 3 L33: 6.3902 L12: -1.2335 REMARK 3 L13: -2.1366 L23: 1.2711 REMARK 3 S TENSOR REMARK 3 S11: 0.0127 S12: -0.2335 S13: 0.0816 REMARK 3 S21: 0.1974 S22: 0.0460 S23: -0.2068 REMARK 3 S31: -0.1051 S32: 0.0746 S33: -0.0587 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 148 B 215 REMARK 3 ORIGIN FOR THE GROUP (A): -44.8203 6.9078 -54.5318 REMARK 3 T TENSOR REMARK 3 T11: 0.2480 T22: 0.2556 REMARK 3 T33: 0.0280 T12: 0.0300 REMARK 3 T13: -0.0494 T23: -0.0531 REMARK 3 L TENSOR REMARK 3 L11: 4.5743 L22: 1.6712 REMARK 3 L33: 7.7937 L12: -0.1450 REMARK 3 L13: -3.9166 L23: -0.1447 REMARK 3 S TENSOR REMARK 3 S11: -0.0211 S12: 0.9185 S13: -0.1650 REMARK 3 S21: -0.6020 S22: -0.1998 S23: 0.1687 REMARK 3 S31: 0.0811 S32: -0.4677 S33: 0.2209 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): -34.5813 16.3692 -39.8828 REMARK 3 T TENSOR REMARK 3 T11: 0.0583 T22: 0.0584 REMARK 3 T33: 0.0209 T12: -0.0348 REMARK 3 T13: 0.0048 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 4.0734 L22: 7.7692 REMARK 3 L33: 1.2114 L12: 3.7872 REMARK 3 L13: 0.0736 L23: 0.6101 REMARK 3 S TENSOR REMARK 3 S11: -0.0473 S12: 0.0271 S13: 0.0947 REMARK 3 S21: -0.3770 S22: -0.0408 S23: -0.0945 REMARK 3 S31: -0.1596 S32: 0.0643 S33: 0.0881 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): -33.1635 16.4958 -40.7212 REMARK 3 T TENSOR REMARK 3 T11: 0.0351 T22: 0.0505 REMARK 3 T33: 0.0442 T12: -0.0237 REMARK 3 T13: 0.0143 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 3.7234 L22: 7.8941 REMARK 3 L33: 1.9474 L12: 3.3393 REMARK 3 L13: 0.1521 L23: 0.6950 REMARK 3 S TENSOR REMARK 3 S11: 0.0555 S12: -0.0730 S13: 0.0054 REMARK 3 S21: -0.1495 S22: -0.0080 S23: -0.4561 REMARK 3 S31: -0.1108 S32: 0.1873 S33: -0.0475 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): -45.9570 14.6354 -5.4009 REMARK 3 T TENSOR REMARK 3 T11: 0.0877 T22: 0.1756 REMARK 3 T33: 0.0185 T12: 0.0871 REMARK 3 T13: 0.0015 T23: -0.0370 REMARK 3 L TENSOR REMARK 3 L11: 2.5753 L22: 2.0513 REMARK 3 L33: 6.0800 L12: 0.9595 REMARK 3 L13: 1.5021 L23: 0.9154 REMARK 3 S TENSOR REMARK 3 S11: -0.0314 S12: 0.1302 S13: -0.0839 REMARK 3 S21: -0.1767 S22: 0.0540 S23: -0.1463 REMARK 3 S31: 0.1092 S32: 0.1060 S33: -0.0226 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): -63.4992 23.7365 23.8576 REMARK 3 T TENSOR REMARK 3 T11: 0.3124 T22: 0.2711 REMARK 3 T33: 0.0081 T12: 0.0105 REMARK 3 T13: 0.0088 T23: -0.0308 REMARK 3 L TENSOR REMARK 3 L11: 3.6981 L22: 2.8069 REMARK 3 L33: 6.4578 L12: 0.4901 REMARK 3 L13: 1.0826 L23: -0.8501 REMARK 3 S TENSOR REMARK 3 S11: 0.0733 S12: -0.7515 S13: 0.0784 REMARK 3 S21: 0.8776 S22: -0.2081 S23: 0.0596 REMARK 3 S31: -0.2859 S32: -0.0112 S33: 0.1348 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): -52.7839 13.9836 9.1459 REMARK 3 T TENSOR REMARK 3 T11: 0.0820 T22: 0.0874 REMARK 3 T33: 0.0367 T12: 0.0482 REMARK 3 T13: -0.0190 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 3.1538 L22: 7.5785 REMARK 3 L33: 1.7035 L12: -4.0276 REMARK 3 L13: -0.2929 L23: 0.6306 REMARK 3 S TENSOR REMARK 3 S11: -0.0828 S12: -0.0088 S13: -0.1276 REMARK 3 S21: 0.4425 S22: -0.0090 S23: -0.0796 REMARK 3 S31: 0.1531 S32: 0.0531 S33: 0.0918 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): -51.3591 13.9083 9.9527 REMARK 3 T TENSOR REMARK 3 T11: 0.0571 T22: 0.0792 REMARK 3 T33: 0.0589 T12: 0.0458 REMARK 3 T13: -0.0108 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 4.4284 L22: 7.3619 REMARK 3 L33: 1.8368 L12: -3.7394 REMARK 3 L13: -0.5692 L23: 1.1052 REMARK 3 S TENSOR REMARK 3 S11: 0.0661 S12: 0.0540 S13: -0.0590 REMARK 3 S21: 0.0988 S22: -0.0286 S23: -0.4192 REMARK 3 S31: 0.0851 S32: 0.1346 S33: -0.0374 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: ARP/WARP WAS USED IN ATOM UPDATE/MAP REMARK 3 IMPROVEMENT MODE. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. REMARK 3 MODEL GEOMETRY WAS ASSESSED WITH MOLPROBITY. REMARK 4 REMARK 4 6C1A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000231923. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31675 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 35.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.66300 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 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG-3350, 0.2 M AMMONIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, 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 PRO A 215 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 GLY B 147 REMARK 465 SER B 216 REMARK 465 LYS B 217 REMARK 465 LEU B 218 REMARK 465 GLN B 219 REMARK 465 LYS B 220 REMARK 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 GLY A 147 N 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 SER A 171 OG REMARK 470 LYS A 174 CE NZ REMARK 470 SER A 183 OG REMARK 470 LYS A 185 CD CE NZ REMARK 470 LYS A 212 CE NZ 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 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 SER B 183 OG REMARK 470 LYS B 185 CG CD CE NZ REMARK 470 LYS B 186 NZ REMARK 470 SER B 205 OG REMARK 470 LYS B 212 CD CE NZ REMARK 470 MET B 214 CG SD CE REMARK 470 PRO B 215 CA C O CB CG CD 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 CD1 CD2 REMARK 470 LYS E 174 CD CE NZ REMARK 470 SER E 183 OG REMARK 470 LYS E 185 CD CE NZ 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 LYS F 160 CG CD 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 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 PRO E 215 C - N - CA ANGL. DEV. = 11.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DA D 5 and 5CM D 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 D 6 and DA D REMARK 800 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DA H 5 and 5CM H 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 H 6 and DA H REMARK 800 7 DBREF 6C1A A 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1A B 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1A C 1 12 PDB 6C1A 6C1A 1 12 DBREF 6C1A D 1 12 PDB 6C1A 6C1A 1 12 DBREF 6C1A E 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1A F 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1A G 1 12 PDB 6C1A 6C1A 1 12 DBREF 6C1A H 1 12 PDB 6C1A 6C1A 1 12 SEQADV 6C1A GLY A 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C1A GLY B 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C1A GLY E 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C1A 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 DA DT DG DT DA DG DG DC SEQRES 1 D 12 DG DC DC DT DA 5CM DA DT 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 DA DT DG DT DA DG DG DC SEQRES 1 H 12 DG DC DC DT DA 5CM DA DT DT DC DC DG HET 5CM D 6 20 HET 5CM H 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 A 310 1 HET UNX A 311 1 HET UNX A 312 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 B 307 1 HET UNX B 308 1 HET UNX B 309 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 D 102 1 HET UNX D 103 1 HET UNX D 104 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 E 308 1 HET UNX E 309 1 HET UNX E 310 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 G 105 1 HET UNX G 106 1 HET UNX G 107 1 HET UNX H 101 1 HET UNX H 102 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 4 5CM 2(C10 H16 N3 O7 P) FORMUL 9 UNX 52(X) FORMUL 61 HOH *115(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 ASP A 176 N VAL A 164 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 ASP F 176 N VAL F 164 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 LINK O3' DA D 5 P 5CM D 6 1555 1555 1.62 LINK O3' 5CM D 6 P DA D 7 1555 1555 1.58 LINK O3' DA H 5 P 5CM H 6 1555 1555 1.64 LINK O3' 5CM H 6 P DA H 7 1555 1555 1.57 SITE 1 AC1 13 ARG A 188 SER A 189 PRO A 191 ARG A 195 SITE 2 AC1 13 HOH A 409 HOH A 411 DG C 7 DT C 8 SITE 3 AC1 13 DA C 9 DT D 4 DA D 7 HOH D 203 SITE 4 AC1 13 HOH D 205 SITE 1 AC2 13 ARG A 188 SER A 189 ARG A 195 HOH A 411 SITE 2 AC2 13 DA C 5 DT C 6 DG C 7 DA D 5 SITE 3 AC2 13 DT D 8 HOH D 203 HOH D 205 HOH D 206 SITE 4 AC2 13 HOH D 210 SITE 1 AC3 14 ARG E 188 SER E 189 LYS E 190 PRO E 191 SITE 2 AC3 14 ARG E 195 HOH E 409 DG G 7 DT G 8 SITE 3 AC3 14 DA G 9 DT H 4 DA H 7 HOH H 203 SITE 4 AC3 14 HOH H 207 HOH H 211 SITE 1 AC4 12 ARG E 188 SER E 189 ARG E 195 HOH E 409 SITE 2 AC4 12 DA G 5 DT G 6 DG G 7 DA H 5 SITE 3 AC4 12 DT H 8 HOH H 203 HOH H 209 HOH H 211 CRYST1 36.533 39.875 105.151 83.97 85.70 62.75 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 0.027373 -0.014098 -0.000935 0.00000 SCALE2 0.000000 0.028209 -0.002259 0.00000 SCALE3 0.000000 0.000000 0.009567 0.00000