HEADER DNA BINDING PROTEIN/DNA 06-FEB-18 6CC8 TITLE CRYSTAL STRUCTURE MBD3 MBD DOMAIN IN COMPLEX WITH METHYLATED CPG DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MBD DOMAIN (UNP RESIDUES 1-71); COMPND 5 SYNONYM: METHYL-CPG-BINDING PROTEIN MBD3; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: METHYLATED CPG DNA; 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: MBD3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-GSTLIC; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: DODECANUCLEOTIDE KEYWDS STRUCTURAL GENOMICS CONSORTIUM, SGC, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.LIU,W.TEMPEL,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,J.MIN,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (SGC) REVDAT 4 04-OCT-23 6CC8 1 REMARK REVDAT 3 04-SEP-19 6CC8 1 JRNL REVDAT 2 22-MAY-19 6CC8 1 COMPND JRNL HET HETNAM REVDAT 2 2 1 FORMUL ATOM REVDAT 1 04-APR-18 6CC8 0 JRNL AUTH K.LIU,M.LEI,Z.WU,B.GAN,H.CHENG,Y.LI,J.MIN JRNL TITL STRUCTURAL ANALYSES REVEAL THAT MBD3 IS A METHYLATED CG JRNL TITL 2 BINDER. JRNL REF FEBS J. V. 286 3240 2019 JRNL REFN ISSN 1742-464X JRNL PMID 30980593 JRNL DOI 10.1111/FEBS.14850 REMARK 2 REMARK 2 RESOLUTION. 1.95 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23724 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 RESOLUTION SHELLS REMARK 3 (SFTOOLS) REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1436 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1775 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1126 REMARK 3 NUCLEIC ACID ATOMS : 976 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.54000 REMARK 3 B22 (A**2) : 0.80000 REMARK 3 B33 (A**2) : -0.27000 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): 0.170 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.156 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.132 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.689 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2258 ; 0.014 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 1614 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3247 ; 1.652 ; 1.617 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3743 ; 1.260 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 144 ; 5.600 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 51 ;28.405 ;19.412 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 197 ;12.062 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;17.330 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 292 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1865 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 512 ; 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): 570 ; 1.783 ; 2.368 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 569 ; 1.783 ; 2.364 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 710 ; 2.769 ; 3.527 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 : 6 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 1 A 71 REMARK 3 ORIGIN FOR THE GROUP (A): -23.4294 -4.7085 54.8601 REMARK 3 T TENSOR REMARK 3 T11: 0.2142 T22: 0.1782 REMARK 3 T33: 0.0210 T12: 0.0107 REMARK 3 T13: 0.0135 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 2.4744 L22: 3.5152 REMARK 3 L33: 4.4811 L12: 0.3020 REMARK 3 L13: -0.7392 L23: -2.0089 REMARK 3 S TENSOR REMARK 3 S11: 0.0083 S12: -0.1273 S13: -0.1777 REMARK 3 S21: 0.1344 S22: 0.0527 S23: 0.0710 REMARK 3 S31: 0.2197 S32: -0.3109 S33: -0.0610 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 71 REMARK 3 ORIGIN FOR THE GROUP (A): -20.3097 6.7967 10.3602 REMARK 3 T TENSOR REMARK 3 T11: 0.1920 T22: 0.1434 REMARK 3 T33: 0.0274 T12: -0.0224 REMARK 3 T13: 0.0285 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 2.7592 L22: 3.1747 REMARK 3 L33: 4.3792 L12: -0.6027 REMARK 3 L13: 0.6383 L23: -1.7675 REMARK 3 S TENSOR REMARK 3 S11: 0.0461 S12: 0.1226 S13: 0.2067 REMARK 3 S21: -0.1806 S22: 0.0695 S23: 0.0699 REMARK 3 S31: -0.2310 S32: -0.1989 S33: -0.1155 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): -18.8825 8.2276 46.4850 REMARK 3 T TENSOR REMARK 3 T11: 0.1922 T22: 0.2258 REMARK 3 T33: 0.1501 T12: 0.0549 REMARK 3 T13: 0.0435 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 3.9286 L22: 4.5481 REMARK 3 L33: 1.6146 L12: -3.6834 REMARK 3 L13: -0.2993 L23: -0.3219 REMARK 3 S TENSOR REMARK 3 S11: 0.0020 S12: 0.0496 S13: 0.3829 REMARK 3 S21: -0.1249 S22: -0.0613 S23: -0.1461 REMARK 3 S31: -0.0081 S32: 0.0014 S33: 0.0593 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): -18.8107 7.3695 45.1612 REMARK 3 T TENSOR REMARK 3 T11: 0.1741 T22: 0.2159 REMARK 3 T33: 0.1161 T12: 0.0692 REMARK 3 T13: 0.0970 T23: 0.0179 REMARK 3 L TENSOR REMARK 3 L11: 6.2491 L22: 2.4422 REMARK 3 L33: 1.7277 L12: -1.5107 REMARK 3 L13: 1.4651 L23: 0.3652 REMARK 3 S TENSOR REMARK 3 S11: 0.0155 S12: 0.2951 S13: 0.3455 REMARK 3 S21: -0.0277 S22: -0.1512 S23: -0.1632 REMARK 3 S31: -0.0189 S32: 0.0087 S33: 0.1357 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 1 E 12 REMARK 3 ORIGIN FOR THE GROUP (A): -15.9889 -6.1412 18.9401 REMARK 3 T TENSOR REMARK 3 T11: 0.1166 T22: 0.1827 REMARK 3 T33: 0.1574 T12: -0.0667 REMARK 3 T13: -0.0040 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 3.8699 L22: 4.1274 REMARK 3 L33: 2.0485 L12: 3.2512 REMARK 3 L13: 0.4073 L23: -0.5999 REMARK 3 S TENSOR REMARK 3 S11: -0.0562 S12: -0.0091 S13: -0.4305 REMARK 3 S21: 0.0020 S22: -0.0204 S23: -0.1255 REMARK 3 S31: -0.0089 S32: 0.0276 S33: 0.0766 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 1 F 12 REMARK 3 ORIGIN FOR THE GROUP (A): -15.8663 -5.3088 20.2656 REMARK 3 T TENSOR REMARK 3 T11: 0.1267 T22: 0.1970 REMARK 3 T33: 0.1300 T12: -0.0600 REMARK 3 T13: -0.0637 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 6.1252 L22: 3.2210 REMARK 3 L33: 1.7577 L12: 2.1094 REMARK 3 L13: -1.2738 L23: 0.0394 REMARK 3 S TENSOR REMARK 3 S11: 0.1021 S12: -0.3004 S13: -0.2897 REMARK 3 S21: 0.0558 S22: -0.1164 S23: -0.0868 REMARK 3 S31: 0.0564 S32: 0.0617 S33: 0.0144 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: MODEL WAS ORIGINALLY REFINED AGAINST REMARK 3 DATA COLLECTED ON AN ISOMORPHOUS CRYSTAL. THAT STRUCTURE WAS REMARK 3 SOLVED BY MOLECULAR REPLACEMENT USING PHASER AND MOLREP TO REMARK 3 POSITION FIRST AND SECOND COPY OF THE COMPLEX, RESPECTIVELY. REMARK 3 REFMAC WAS USED DURING INTERMEDIATE REFINEMENT. COOT WAS USED REMARK 3 FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS ASSESSED ON REMARK 3 THE MOLPROBITY SERVER. REMARK 4 REMARK 4 6CC8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232534. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.97923 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25160 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 35.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.76100 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, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 6C2K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2 M SODIUM CHLORIDE, REMARK 280 0.1 M HEPES, 5% ETHYLENE GLYCOL, PH 7.5, VAPOR DIFFUSION, 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 35.77500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.32000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.77500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.32000 REMARK 290 SMTRY3 4 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: 3820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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: 3790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLY B -1 REMARK 465 SER B 0 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 MET A 1 CG SD CE REMARK 470 GLU A 2 CG CD OE1 OE2 REMARK 470 LYS A 4 CE NZ REMARK 470 GLU A 7 CG CD OE1 OE2 REMARK 470 GLN A 13 CG CD OE1 NE2 REMARK 470 LEU A 26 CD1 CD2 REMARK 470 LYS A 41 NZ REMARK 470 LEU A 53 CD1 CD2 REMARK 470 MET B 1 CG SD CE REMARK 470 GLU B 2 CG CD OE1 OE2 REMARK 470 GLU B 7 CG CD OE1 OE2 REMARK 470 GLN B 13 CD OE1 NE2 REMARK 470 ARG B 23 CG CD NE CZ NH1 NH2 DBREF 6CC8 A 1 71 UNP O95983 MBD3_HUMAN 1 71 DBREF 6CC8 B 1 71 UNP O95983 MBD3_HUMAN 1 71 DBREF 6CC8 C 1 12 PDB 6CC8 6CC8 1 12 DBREF 6CC8 D 1 12 PDB 6CC8 6CC8 1 12 DBREF 6CC8 E 1 12 PDB 6CC8 6CC8 1 12 DBREF 6CC8 F 1 12 PDB 6CC8 6CC8 1 12 SEQADV 6CC8 GLY A -1 UNP O95983 EXPRESSION TAG SEQADV 6CC8 SER A 0 UNP O95983 EXPRESSION TAG SEQADV 6CC8 GLY B -1 UNP O95983 EXPRESSION TAG SEQADV 6CC8 SER B 0 UNP O95983 EXPRESSION TAG SEQRES 1 A 73 GLY SER MET GLU ARG LYS ARG TRP GLU CYS PRO ALA LEU SEQRES 2 A 73 PRO GLN GLY TRP GLU ARG GLU GLU VAL PRO ARG ARG SER SEQRES 3 A 73 GLY LEU SER ALA GLY HIS ARG ASP VAL PHE TYR TYR SER SEQRES 4 A 73 PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU ALA SEQRES 5 A 73 ARG TYR LEU GLY GLY SER MET ASP LEU SER THR PHE ASP SEQRES 6 A 73 PHE ARG THR GLY LYS MET LEU MET SEQRES 1 B 73 GLY SER MET GLU ARG LYS ARG TRP GLU CYS PRO ALA LEU SEQRES 2 B 73 PRO GLN GLY TRP GLU ARG GLU GLU VAL PRO ARG ARG SER SEQRES 3 B 73 GLY LEU SER ALA GLY HIS ARG ASP VAL PHE TYR TYR SER SEQRES 4 B 73 PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU ALA SEQRES 5 B 73 ARG TYR LEU GLY GLY SER MET ASP LEU SER THR PHE ASP SEQRES 6 B 73 PHE ARG THR GLY LYS MET LEU MET SEQRES 1 C 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 D 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 E 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 F 12 DG DC DC DA DA 5CM DG DT DT DG DG DC HET 5CM C 6 20 HET 5CM D 6 20 HET 5CM E 6 20 HET 5CM F 6 20 HET UNX A 101 1 HET UNX A 102 1 HET UNX A 103 1 HET UNX B 101 1 HET UNX B 102 1 HET UNX B 103 1 HET UNX B 104 1 HET UNX C 101 1 HET UNX C 102 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 UNX UNKNOWN ATOM OR ION FORMUL 3 5CM 4(C10 H16 N3 O7 P) FORMUL 7 UNX 12(X) FORMUL 19 HOH *64(H2 O) HELIX 1 AA1 SER A 45 GLY A 54 1 10 HELIX 2 AA2 SER B 45 GLY B 54 1 10 SHEET 1 AA1 4 LYS A 4 GLU A 7 0 SHEET 2 AA1 4 GLU A 16 PRO A 21 -1 O ARG A 17 N TRP A 6 SHEET 3 AA1 4 ARG A 31 TYR A 36 -1 O TYR A 36 N GLU A 16 SHEET 4 AA1 4 LYS A 42 PHE A 43 -1 O PHE A 43 N TYR A 35 SHEET 1 AA2 2 PHE A 62 ASP A 63 0 SHEET 2 AA2 2 LYS A 68 MET A 69 -1 O LYS A 68 N ASP A 63 SHEET 1 AA3 4 LYS B 4 GLU B 7 0 SHEET 2 AA3 4 GLU B 16 PRO B 21 -1 O ARG B 17 N TRP B 6 SHEET 3 AA3 4 ARG B 31 TYR B 36 -1 O PHE B 34 N GLU B 18 SHEET 4 AA3 4 LYS B 42 PHE B 43 -1 O PHE B 43 N TYR B 35 SHEET 1 AA4 2 PHE B 62 ASP B 63 0 SHEET 2 AA4 2 LYS B 68 MET B 69 -1 O LYS B 68 N ASP B 63 LINK O3' DA C 5 P 5CM C 6 1555 1555 1.62 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.61 LINK O3' DA D 5 P 5CM D 6 1555 1555 1.63 LINK O3' 5CM D 6 P DG D 7 1555 1555 1.58 LINK O3' DA E 5 P 5CM E 6 1555 1555 1.62 LINK O3' 5CM E 6 P DG E 7 1555 1555 1.63 LINK O3' DA F 5 P 5CM F 6 1555 1555 1.59 LINK O3' 5CM F 6 P DG F 7 1555 1555 1.59 CRYST1 71.550 36.640 130.930 90.00 92.77 90.00 C 1 2 1 16 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 0.013976 0.000000 0.000676 0.00000 SCALE2 0.000000 0.027293 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007647 0.00000