PDB Short entry for 6C1U HEADER DNA BINDING PROTEIN/DNA 05-JAN-18 6C1U TITLE MBD2 IN COMPLEX WITH A DEOXY-OLIGONUCLEOTIDE 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 6C1U 1 REMARK REVDAT 4 13-MAR-24 6C1U 1 REMARK REVDAT 3 23-MAY-18 6C1U 1 JRNL REVDAT 2 18-APR-18 6C1U 1 JRNL REVDAT 1 14-FEB-18 6C1U 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) : 35.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 21914 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.600 REMARK 3 FREE R VALUE TEST SET COUNT : 808 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) : 1698 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2035 REMARK 3 NUCLEIC ACID ATOMS : 974 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.53000 REMARK 3 B22 (A**2) : 0.87000 REMARK 3 B33 (A**2) : -1.68000 REMARK 3 B12 (A**2) : -0.83000 REMARK 3 B13 (A**2) : 0.98000 REMARK 3 B23 (A**2) : -0.78000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.310 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.241 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.214 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.714 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3176 ; 0.014 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 2407 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4484 ; 1.793 ; 1.696 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5571 ; 1.219 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 269 ; 6.669 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;28.992 ;21.139 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 329 ;14.053 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;18.842 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 427 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2922 ; 0.013 ; 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): 1084 ; 1.353 ; 3.113 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1082 ; 1.352 ; 3.111 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1350 ; 2.170 ; 4.658 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): -27.7505 16.3216 -25.6641 REMARK 3 T TENSOR REMARK 3 T11: 0.0696 T22: 0.1923 REMARK 3 T33: 0.0478 T12: -0.0896 REMARK 3 T13: 0.0145 T23: -0.0391 REMARK 3 L TENSOR REMARK 3 L11: 2.7073 L22: 3.3979 REMARK 3 L33: 7.0130 L12: -1.1763 REMARK 3 L13: -0.0485 L23: 1.4822 REMARK 3 S TENSOR REMARK 3 S11: -0.0229 S12: -0.1635 S13: -0.0016 REMARK 3 S21: 0.1818 S22: 0.1297 S23: -0.2299 REMARK 3 S31: -0.1974 S32: 0.2914 S33: -0.1068 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): -45.1539 8.4864 -55.0331 REMARK 3 T TENSOR REMARK 3 T11: 0.3816 T22: 0.3122 REMARK 3 T33: 0.0897 T12: -0.0498 REMARK 3 T13: -0.0511 T23: -0.0278 REMARK 3 L TENSOR REMARK 3 L11: 3.3243 L22: 1.4553 REMARK 3 L33: 8.0106 L12: -1.1754 REMARK 3 L13: -3.8205 L23: 0.2675 REMARK 3 S TENSOR REMARK 3 S11: 0.1474 S12: 0.5741 S13: -0.0071 REMARK 3 S21: -0.6020 S22: -0.1880 S23: 0.1494 REMARK 3 S31: 0.0964 S32: -0.3861 S33: 0.0406 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): -34.9360 17.9478 -39.8557 REMARK 3 T TENSOR REMARK 3 T11: 0.0838 T22: 0.0787 REMARK 3 T33: 0.0274 T12: -0.0459 REMARK 3 T13: 0.0025 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 4.2443 L22: 7.3728 REMARK 3 L33: 1.6847 L12: 4.3699 REMARK 3 L13: 0.4410 L23: 1.6833 REMARK 3 S TENSOR REMARK 3 S11: -0.0711 S12: 0.0178 S13: 0.2648 REMARK 3 S21: -0.4589 S22: 0.0221 S23: 0.2951 REMARK 3 S31: -0.3029 S32: 0.1228 S33: 0.0490 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): -33.6604 17.6424 -40.7069 REMARK 3 T TENSOR REMARK 3 T11: 0.0906 T22: 0.0579 REMARK 3 T33: 0.0673 T12: -0.0430 REMARK 3 T13: 0.0309 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 3.5572 L22: 8.0237 REMARK 3 L33: 1.5917 L12: 3.1904 REMARK 3 L13: 0.3536 L23: 0.9449 REMARK 3 S TENSOR REMARK 3 S11: 0.0356 S12: -0.0355 S13: 0.0434 REMARK 3 S21: -0.2222 S22: -0.0817 S23: -0.3429 REMARK 3 S31: -0.1087 S32: 0.0695 S33: 0.0461 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 147 E 215 REMARK 3 ORIGIN FOR THE GROUP (A): -46.2849 14.3515 -5.5360 REMARK 3 T TENSOR REMARK 3 T11: 0.0857 T22: 0.1716 REMARK 3 T33: 0.0611 T12: 0.0631 REMARK 3 T13: 0.0218 T23: -0.0365 REMARK 3 L TENSOR REMARK 3 L11: 3.3864 L22: 2.9333 REMARK 3 L33: 7.2430 L12: 1.2771 REMARK 3 L13: 0.7575 L23: 1.1323 REMARK 3 S TENSOR REMARK 3 S11: -0.0967 S12: 0.2099 S13: -0.0518 REMARK 3 S21: -0.2635 S22: 0.2198 S23: -0.1259 REMARK 3 S31: 0.1128 S32: 0.2159 S33: -0.1232 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 147 F 215 REMARK 3 ORIGIN FOR THE GROUP (A): -64.8666 23.0714 23.8661 REMARK 3 T TENSOR REMARK 3 T11: 0.3458 T22: 0.2809 REMARK 3 T33: 0.1620 T12: 0.0137 REMARK 3 T13: 0.0545 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 2.4783 L22: 2.3374 REMARK 3 L33: 9.4358 L12: 0.8814 REMARK 3 L13: 0.7204 L23: 1.5078 REMARK 3 S TENSOR REMARK 3 S11: 0.1484 S12: -0.5573 S13: -0.0573 REMARK 3 S21: 0.7506 S22: -0.1010 S23: 0.0502 REMARK 3 S31: -0.1983 S32: 0.0976 S33: -0.0474 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): -53.2773 12.6426 8.9417 REMARK 3 T TENSOR REMARK 3 T11: 0.1742 T22: 0.0598 REMARK 3 T33: 0.0953 T12: 0.0403 REMARK 3 T13: -0.0202 T23: 0.0555 REMARK 3 L TENSOR REMARK 3 L11: 3.2346 L22: 7.0006 REMARK 3 L33: 2.5787 L12: -4.0727 REMARK 3 L13: -0.0725 L23: 1.8479 REMARK 3 S TENSOR REMARK 3 S11: -0.1268 S12: -0.0039 S13: -0.2107 REMARK 3 S21: 0.6031 S22: 0.0719 S23: 0.1346 REMARK 3 S31: 0.2346 S32: 0.1347 S33: 0.0549 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): -52.0080 13.0161 9.7083 REMARK 3 T TENSOR REMARK 3 T11: 0.0884 T22: 0.0414 REMARK 3 T33: 0.1179 T12: 0.0517 REMARK 3 T13: 0.0227 T23: 0.0327 REMARK 3 L TENSOR REMARK 3 L11: 4.0561 L22: 8.4543 REMARK 3 L33: 2.0953 L12: -4.0361 REMARK 3 L13: -0.3827 L23: 1.4342 REMARK 3 S TENSOR REMARK 3 S11: 0.0096 S12: 0.0448 S13: -0.0740 REMARK 3 S21: 0.2860 S22: -0.0322 S23: -0.2483 REMARK 3 S31: 0.1434 S32: 0.1003 S33: 0.0226 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 6C1U 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_1000230209. 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 : NULL 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) : 0.97934 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 : 33843 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 35.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.57800 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 (%): 56.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG-3350, 0.2 M POTASSIUM REMARK 280 DIHYDROGEN PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 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 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 LYS A 174 CD 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 N CB 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 204 OG REMARK 470 SER B 205 OG REMARK 470 LYS B 212 CD CE NZ REMARK 470 MET B 214 CG SD CE REMARK 470 GLY E 147 N 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 LYS E 174 CG CD CE NZ REMARK 470 SER E 183 OG REMARK 470 LYS E 185 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 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 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 VAL F 201 CG1 CG2 REMARK 470 SER F 204 OG REMARK 470 SER F 205 OG REMARK 470 LYS F 212 NZ REMARK 470 PRO F 215 CA 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 B 153 C - N - CA ANGL. DEV. = 10.2 DEGREES REMARK 500 PRO E 215 C - N - CA ANGL. DEV. = 10.2 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 6C1U A 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1U B 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1U C 1 12 PDB 6C1U 6C1U 1 12 DBREF 6C1U D 1 12 PDB 6C1U 6C1U 1 12 DBREF 6C1U E 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1U F 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6C1U G 1 12 PDB 6C1U 6C1U 1 12 DBREF 6C1U H 1 12 PDB 6C1U 6C1U 1 12 SEQADV 6C1U GLY A 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C1U GLY B 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C1U GLY E 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6C1U 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 DG DG DG DC SEQRES 1 D 12 DG DC DC DC DA 5CM 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 DG DG DG DC SEQRES 1 H 12 DG DC DC DC DA 5CM DA DC 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 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 B 310 1 HET UNX B 311 1 HET UNX B 312 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 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 F 301 1 HET UNX F 302 1 HET UNX F 303 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 42(X) FORMUL 51 HOH *25(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 SER E 189 GLY E 198 1 10 HELIX 5 AA5 ASN E 199 VAL E 201 5 3 HELIX 6 AA6 SER F 189 GLY F 198 1 10 HELIX 7 AA7 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 PHE A 180 N LYS A 160 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 PHE E 180 N LYS E 160 SHEET 4 AA5 4 LYS E 186 PHE E 187 -1 O PHE E 187 N TYR E 179 SHEET 1 AA6 4 MET F 150 ASP F 151 0 SHEET 2 AA6 4 LYS F 160 ILE F 165 -1 O LYS F 161 N MET F 150 SHEET 3 AA6 4 SER F 175 PHE F 180 -1 O ASP F 176 N VAL F 164 SHEET 4 AA6 4 LYS F 186 PHE F 187 -1 O PHE F 187 N TYR F 179 LINK O3' DA D 5 P 5CM D 6 1555 1555 1.63 LINK O3' 5CM D 6 P DA D 7 1555 1555 1.61 LINK O3' DA H 5 P 5CM H 6 1555 1555 1.58 LINK O3' 5CM H 6 P DA H 7 1555 1555 1.59 SITE 1 AC1 9 ARG A 188 SER A 189 PRO A 191 ARG A 195 SITE 2 AC1 9 DG C 7 DT C 8 DG C 9 DC D 4 SITE 3 AC1 9 DA D 7 SITE 1 AC2 8 ARG A 188 SER A 189 ARG A 195 DG C 5 SITE 2 AC2 8 DT C 6 DG C 7 DA D 5 DC D 8 SITE 1 AC3 10 ARG E 188 SER E 189 PRO E 191 ARG E 195 SITE 2 AC3 10 HOH E 403 DG G 7 DT G 8 DG G 9 SITE 3 AC3 10 DC H 4 DA H 7 SITE 1 AC4 9 ARG E 188 SER E 189 ARG E 195 HOH E 403 SITE 2 AC4 9 DG G 5 DT G 6 DG G 7 DA H 5 SITE 3 AC4 9 DC H 8 CRYST1 36.912 40.015 105.890 84.48 85.91 62.77 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 0.027091 -0.013941 -0.000943 0.00000 SCALE2 0.000000 0.028105 -0.002018 0.00000 SCALE3 0.000000 0.000000 0.009492 0.00000