HEADER TRANSCRIPTION 07-FEB-18 6CCG 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: RESIDUES 1-71; COMPND 5 SYNONYM: METHYL-CPG-BINDING PROTEIN MBD3; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-GSTLIC; 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 DNA CONSTRUCT KEYWDS STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSCRIPTION 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 13-MAR-24 6CCG 1 REMARK REVDAT 3 04-SEP-19 6CCG 1 JRNL REVDAT 2 22-MAY-19 6CCG 1 JRNL REVDAT 1 09-MAY-18 6CCG 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 25763 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1536 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1878 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1144 REMARK 3 NUCLEIC ACID ATOMS : 976 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.14000 REMARK 3 B22 (A**2) : 1.39000 REMARK 3 B33 (A**2) : -0.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.33000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.159 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.217 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2322 ; 0.015 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 1659 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3348 ; 1.543 ; 1.633 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3872 ; 1.190 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 147 ; 5.368 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 53 ;25.590 ;20.189 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 212 ;10.306 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.751 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 305 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1921 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 533 ; 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): 578 ; 1.361 ; 2.425 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 577 ; 1.362 ; 2.422 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 722 ; 2.202 ; 3.622 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 0 A 80 REMARK 3 ORIGIN FOR THE GROUP (A): -23.1226 -4.6033 54.5264 REMARK 3 T TENSOR REMARK 3 T11: 0.2576 T22: 0.1425 REMARK 3 T33: 0.0152 T12: 0.0317 REMARK 3 T13: 0.0134 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 2.6557 L22: 3.6366 REMARK 3 L33: 4.0551 L12: 0.6015 REMARK 3 L13: -0.3977 L23: -2.3473 REMARK 3 S TENSOR REMARK 3 S11: 0.0026 S12: -0.1839 S13: -0.1634 REMARK 3 S21: 0.0333 S22: 0.0396 S23: 0.0573 REMARK 3 S31: 0.3074 S32: -0.2993 S33: -0.0421 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 0 B 80 REMARK 3 ORIGIN FOR THE GROUP (A): -20.3238 6.7182 10.5204 REMARK 3 T TENSOR REMARK 3 T11: 0.2295 T22: 0.1279 REMARK 3 T33: 0.0164 T12: -0.0311 REMARK 3 T13: 0.0022 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 2.6219 L22: 3.2960 REMARK 3 L33: 5.0865 L12: -0.7989 REMARK 3 L13: 0.4391 L23: -2.2057 REMARK 3 S TENSOR REMARK 3 S11: 0.0132 S12: 0.2102 S13: 0.1530 REMARK 3 S21: -0.1348 S22: 0.0007 S23: 0.0739 REMARK 3 S31: -0.2646 S32: -0.2219 S33: -0.0139 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): -18.5431 8.3830 46.3019 REMARK 3 T TENSOR REMARK 3 T11: 0.2312 T22: 0.1529 REMARK 3 T33: 0.2028 T12: 0.0844 REMARK 3 T13: 0.0295 T23: -0.0479 REMARK 3 L TENSOR REMARK 3 L11: 4.1799 L22: 4.3210 REMARK 3 L33: 2.1503 L12: -4.1819 REMARK 3 L13: 0.9748 L23: -0.7407 REMARK 3 S TENSOR REMARK 3 S11: 0.1031 S12: 0.0417 S13: 0.3944 REMARK 3 S21: -0.1403 S22: -0.1117 S23: -0.2834 REMARK 3 S31: 0.0733 S32: 0.0835 S33: 0.0086 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): -18.6668 7.7648 44.9913 REMARK 3 T TENSOR REMARK 3 T11: 0.2174 T22: 0.1841 REMARK 3 T33: 0.0843 T12: 0.0835 REMARK 3 T13: 0.0683 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 6.1548 L22: 2.2912 REMARK 3 L33: 0.6381 L12: -2.1147 REMARK 3 L13: 1.3276 L23: 0.2322 REMARK 3 S TENSOR REMARK 3 S11: 0.1116 S12: 0.3847 S13: 0.3274 REMARK 3 S21: -0.1850 S22: -0.1887 S23: -0.1300 REMARK 3 S31: 0.0057 S32: 0.0257 S33: 0.0771 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): -15.8571 -6.2955 19.0526 REMARK 3 T TENSOR REMARK 3 T11: 0.1716 T22: 0.1208 REMARK 3 T33: 0.1220 T12: -0.0611 REMARK 3 T13: -0.0376 T23: -0.0522 REMARK 3 L TENSOR REMARK 3 L11: 4.6458 L22: 3.1698 REMARK 3 L33: 1.8201 L12: 3.2847 REMARK 3 L13: -0.3931 L23: -0.6285 REMARK 3 S TENSOR REMARK 3 S11: -0.0067 S12: 0.0720 S13: -0.3844 REMARK 3 S21: 0.0589 S22: -0.0242 S23: -0.1687 REMARK 3 S31: 0.0082 S32: 0.0477 S33: 0.0309 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): -15.9606 -5.6777 20.3715 REMARK 3 T TENSOR REMARK 3 T11: 0.1608 T22: 0.1577 REMARK 3 T33: 0.0926 T12: -0.0808 REMARK 3 T13: -0.0555 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 6.4441 L22: 2.7586 REMARK 3 L33: 1.3685 L12: 2.2223 REMARK 3 L13: -1.1958 L23: -0.2301 REMARK 3 S TENSOR REMARK 3 S11: 0.0993 S12: -0.3761 S13: -0.2477 REMARK 3 S21: 0.1225 S22: -0.1448 S23: -0.1035 REMARK 3 S31: -0.0099 S32: 0.0386 S33: 0.0456 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: COOT WAS USED FOR INTERACTIVE MODEL REMARK 3 BUILDING. MODEL GEOMETRY WAS ASSESSED ON THE MOLPROBITY SERVER. REMARK 4 REMARK 4 6CCG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 0.97911 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 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27299 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 35.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 1.09800 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 8000,0.2M MAGNESIUM CHLORIDE, REMARK 280 0.1M TRIS, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 36.13500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.23000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.13500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.23000 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: 7700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 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 SER A 0 N CB OG REMARK 470 GLU A 2 CG CD OE1 OE2 REMARK 470 ARG A 3 NH1 NH2 REMARK 470 GLN A 13 CG CD OE1 NE2 REMARK 470 LYS A 41 NZ REMARK 470 MET A 71 SD CE REMARK 470 GLU B 2 CG CD OE1 OE2 REMARK 470 GLU B 7 CG CD OE1 OE2 REMARK 470 ARG B 23 CG CD NE CZ NH1 NH2 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 SER A 56 -37.79 -38.70 REMARK 500 REMARK 500 REMARK: NULL DBREF 6CCG A 1 71 UNP O95983 MBD3_HUMAN 1 71 DBREF 6CCG B 1 71 UNP O95983 MBD3_HUMAN 1 71 DBREF 6CCG C 1 12 PDB 6CCG 6CCG 1 12 DBREF 6CCG D 1 12 PDB 6CCG 6CCG 1 12 DBREF 6CCG E 1 12 PDB 6CCG 6CCG 1 12 DBREF 6CCG F 1 12 PDB 6CCG 6CCG 1 12 SEQADV 6CCG GLY A -1 UNP O95983 EXPRESSION TAG SEQADV 6CCG SER A 0 UNP O95983 EXPRESSION TAG SEQADV 6CCG GLY B -1 UNP O95983 EXPRESSION TAG SEQADV 6CCG 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 DG 5CM DG DC DT DG DG DC SEQRES 1 D 12 DG DC DC DA DG 5CM DG DC DT DG DG DC SEQRES 1 E 12 DG DC DC DA DG 5CM DG DC DT DG DG DC SEQRES 1 F 12 DG DC DC DA DG 5CM DG DC DT DG DG DC HET 5CM C 6 31 HET 5CM D 6 20 HET 5CM E 6 30 HET 5CM F 6 20 HET UNX A 101 1 HET UNX A 102 1 HET UNX A 103 1 HET UNX A 104 1 HET UNX B 101 1 HET UNX B 102 1 HET UNX D 101 1 HET UNX F 101 1 HET UNX F 102 1 HET UNX F 103 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 10(X) FORMUL 17 HOH *88(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 PHE A 34 N GLU A 18 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'A DG C 5 P A5CM C 6 1555 1555 1.56 LINK O3'B DG C 5 P B5CM C 6 1555 1555 1.61 LINK O3'A5CM C 6 P DG C 7 1555 1555 1.60 LINK O3'B5CM C 6 P DG C 7 1555 1555 1.58 LINK O3' DG D 5 P 5CM D 6 1555 1555 1.55 LINK O3' 5CM D 6 P DG D 7 1555 1555 1.57 LINK O3'A DG E 5 P A5CM E 6 1555 1555 1.63 LINK O3'B DG E 5 P B5CM E 6 1555 1555 1.57 LINK O3' 5CM E 6 P DG E 7 1555 1555 1.59 LINK O3' DG F 5 P 5CM F 6 1555 1555 1.56 LINK O3' 5CM F 6 P DG F 7 1555 1555 1.58 CRYST1 72.270 36.460 130.840 90.00 92.42 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 0.013837 0.000000 0.000585 0.00000 SCALE2 0.000000 0.027427 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007650 0.00000 CONECT 1252 1292 CONECT 1253 1293 CONECT 1267 1268 1273 1276 1277 CONECT 1268 1267 1269 1274 CONECT 1269 1268 1270 CONECT 1270 1269 1271 1275 CONECT 1271 1270 1272 1273 CONECT 1272 1271 CONECT 1273 1267 1271 CONECT 1274 1268 CONECT 1275 1270 CONECT 1276 1267 1278 1284 CONECT 1277 1267 1279 1285 CONECT 1278 1276 1280 CONECT 1279 1277 1281 CONECT 1280 1278 1282 1286 CONECT 1281 1279 1283 1287 CONECT 1282 1280 1284 1288 CONECT 1283 1281 1285 1289 CONECT 1284 1276 1282 CONECT 1285 1277 1283 CONECT 1286 1280 1298 CONECT 1287 1281 1298 CONECT 1288 1282 1290 CONECT 1289 1283 1291 CONECT 1290 1288 1292 CONECT 1291 1289 1293 CONECT 1292 1252 1290 1294 1296 CONECT 1293 1253 1291 1295 1297 CONECT 1294 1292 CONECT 1295 1293 CONECT 1296 1292 CONECT 1297 1293 CONECT 1298 1286 1287 CONECT 1509 1540 CONECT 1523 1524 1529 1532 CONECT 1524 1523 1525 1530 CONECT 1525 1524 1526 CONECT 1526 1525 1527 1531 CONECT 1527 1526 1528 1529 CONECT 1528 1527 CONECT 1529 1523 1527 CONECT 1530 1524 CONECT 1531 1526 CONECT 1532 1523 1533 1536 CONECT 1533 1532 1534 CONECT 1534 1533 1535 1537 CONECT 1535 1534 1536 1538 CONECT 1536 1532 1535 CONECT 1537 1534 1543 CONECT 1538 1535 1539 CONECT 1539 1538 1540 CONECT 1540 1509 1539 1541 1542 CONECT 1541 1540 CONECT 1542 1540 CONECT 1543 1537 CONECT 1755 1794 CONECT 1756 1795 CONECT 1770 1771 1776 1779 1780 CONECT 1771 1770 1772 1777 CONECT 1772 1771 1773 CONECT 1773 1772 1774 1778 CONECT 1774 1773 1775 1776 CONECT 1775 1774 CONECT 1776 1770 1774 CONECT 1777 1771 CONECT 1778 1773 CONECT 1779 1770 1781 1787 CONECT 1780 1770 1782 1788 CONECT 1781 1779 1783 CONECT 1782 1780 1784 CONECT 1783 1781 1785 1789 CONECT 1784 1782 1786 1789 CONECT 1785 1783 1787 1790 CONECT 1786 1784 1788 1791 CONECT 1787 1779 1785 CONECT 1788 1780 1786 CONECT 1789 1783 1784 1800 CONECT 1790 1785 1792 CONECT 1791 1786 1793 CONECT 1792 1790 1794 CONECT 1793 1791 1795 CONECT 1794 1755 1792 1796 1798 CONECT 1795 1756 1793 1797 1799 CONECT 1796 1794 CONECT 1797 1795 CONECT 1798 1794 CONECT 1799 1795 CONECT 1800 1789 CONECT 2011 2042 CONECT 2025 2026 2031 2034 CONECT 2026 2025 2027 2032 CONECT 2027 2026 2028 CONECT 2028 2027 2029 2033 CONECT 2029 2028 2030 2031 CONECT 2030 2029 CONECT 2031 2025 2029 CONECT 2032 2026 CONECT 2033 2028 CONECT 2034 2025 2035 2038 CONECT 2035 2034 2036 CONECT 2036 2035 2037 2039 CONECT 2037 2036 2038 2040 CONECT 2038 2034 2037 CONECT 2039 2036 2045 CONECT 2040 2037 2041 CONECT 2041 2040 2042 CONECT 2042 2011 2041 2043 2044 CONECT 2043 2042 CONECT 2044 2042 CONECT 2045 2039 MASTER 402 0 14 2 12 0 0 6 2218 6 111 16 END