HEADER DNA BINDING PROTEIN/DNA 23-JUN-17 5W9Q TITLE ZINC FINGER REGION OF MBD1 IN COMPLEX WITH CPG DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ZINC FINGER REGION (UNP RESIDUES 330-388); COMPND 5 SYNONYM: CXXC-TYPE ZINC FINGER PROTEIN 3,METHYL-CPG-BINDING PROTEIN COMPND 6 MBD1,PROTEIN CONTAINING METHYL-CPG-BINDING DOMAIN 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA; COMPND 10 CHAIN: C, D, E, F; COMPND 11 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: MBD1, CXXC3, PCM1; 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 KEYWDS ZINC FINGER, DNA-BINDING, CXXC3, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.LIU,C.XU,W.TEMPEL,J.R.WALKER,C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS, AUTHOR 2 J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 04-OCT-23 5W9Q 1 REMARK REVDAT 3 10-JAN-18 5W9Q 1 JRNL REVDAT 2 03-JAN-18 5W9Q 1 JRNL REVDAT 1 18-OCT-17 5W9Q 0 JRNL AUTH C.XU,K.LIU,M.LEI,A.YANG,Y.LI,T.R.HUGHES,J.MIN JRNL TITL DNA SEQUENCE RECOGNITION OF HUMAN CXXC DOMAINS AND THEIR JRNL TITL 2 STRUCTURAL DETERMINANTS. JRNL REF STRUCTURE V. 26 85 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 29276034 JRNL DOI 10.1016/J.STR.2017.11.022 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 21331 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1306 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1610 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3620 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 839 REMARK 3 NUCLEIC ACID ATOMS : 972 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.63000 REMARK 3 B22 (A**2) : -4.31000 REMARK 3 B33 (A**2) : 4.86000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.36000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.155 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.831 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1976 ; 0.015 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 1370 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2843 ; 1.509 ; 1.497 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3163 ; 1.367 ; 3.010 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 111 ; 6.116 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 42 ;30.855 ;19.762 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 169 ;13.875 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;13.468 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 254 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1564 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 462 ; 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): 441 ; 0.836 ; 1.341 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 440 ; 0.815 ; 1.339 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 547 ; 1.393 ; 1.996 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 333 A 1002 REMARK 3 ORIGIN FOR THE GROUP (A): -11.9756 11.9637 8.0522 REMARK 3 T TENSOR REMARK 3 T11: 0.2670 T22: 0.3848 REMARK 3 T33: 0.0111 T12: 0.0090 REMARK 3 T13: -0.0215 T23: -0.0255 REMARK 3 L TENSOR REMARK 3 L11: 11.4005 L22: 10.1898 REMARK 3 L33: 5.2609 L12: 0.5115 REMARK 3 L13: 1.8513 L23: 2.4065 REMARK 3 S TENSOR REMARK 3 S11: 0.2028 S12: 0.8672 S13: -0.1789 REMARK 3 S21: -0.3113 S22: -0.0829 S23: 0.1841 REMARK 3 S31: -0.0320 S32: 0.4125 S33: -0.1199 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 334 B 1002 REMARK 3 ORIGIN FOR THE GROUP (A): -22.8493 6.1379 -8.3201 REMARK 3 T TENSOR REMARK 3 T11: 0.3228 T22: 0.3971 REMARK 3 T33: 0.0723 T12: -0.0006 REMARK 3 T13: -0.0265 T23: -0.0428 REMARK 3 L TENSOR REMARK 3 L11: 11.8033 L22: 11.0574 REMARK 3 L33: 5.7105 L12: -5.5343 REMARK 3 L13: 2.8391 L23: -0.0954 REMARK 3 S TENSOR REMARK 3 S11: -0.1567 S12: -0.9859 S13: -0.1868 REMARK 3 S21: 0.7590 S22: 0.1650 S23: 0.2868 REMARK 3 S31: 0.1163 S32: -0.4832 S33: -0.0083 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): -10.9649 9.2143 21.6868 REMARK 3 T TENSOR REMARK 3 T11: 0.3431 T22: 0.4207 REMARK 3 T33: 0.0836 T12: -0.0528 REMARK 3 T13: -0.0686 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 11.0223 L22: 4.5220 REMARK 3 L33: 2.6171 L12: 2.2064 REMARK 3 L13: -2.5568 L23: 0.0639 REMARK 3 S TENSOR REMARK 3 S11: 0.1601 S12: -0.9795 S13: -0.1229 REMARK 3 S21: 0.3568 S22: -0.2859 S23: -0.0795 REMARK 3 S31: -0.0774 S32: 0.1998 S33: 0.1258 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): -10.7275 8.0599 20.2980 REMARK 3 T TENSOR REMARK 3 T11: 0.4144 T22: 0.3798 REMARK 3 T33: 0.0877 T12: -0.0345 REMARK 3 T13: -0.0117 T23: -0.0287 REMARK 3 L TENSOR REMARK 3 L11: 12.7418 L22: 10.1215 REMARK 3 L33: 2.7607 L12: 7.2853 REMARK 3 L13: -1.5438 L23: -0.6910 REMARK 3 S TENSOR REMARK 3 S11: -0.0166 S12: -0.1545 S13: -0.9299 REMARK 3 S21: 0.2464 S22: 0.0346 S23: -0.3539 REMARK 3 S31: -0.2036 S32: 0.1161 S33: -0.0179 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): -23.7775 2.3751 -22.1177 REMARK 3 T TENSOR REMARK 3 T11: 0.3527 T22: 0.4462 REMARK 3 T33: 0.2604 T12: 0.0664 REMARK 3 T13: -0.1517 T23: -0.0610 REMARK 3 L TENSOR REMARK 3 L11: 8.5686 L22: 5.0978 REMARK 3 L33: 1.2346 L12: -4.2305 REMARK 3 L13: -1.5325 L23: -0.3521 REMARK 3 S TENSOR REMARK 3 S11: 0.4019 S12: 0.8027 S13: -0.2986 REMARK 3 S21: -0.4818 S22: -0.5227 S23: 0.4273 REMARK 3 S31: -0.0650 S32: -0.0653 S33: 0.1208 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): -23.8870 1.3871 -20.8795 REMARK 3 T TENSOR REMARK 3 T11: 0.4067 T22: 0.4296 REMARK 3 T33: 0.2420 T12: 0.0472 REMARK 3 T13: -0.0621 T23: -0.0379 REMARK 3 L TENSOR REMARK 3 L11: 13.2381 L22: 7.3589 REMARK 3 L33: 2.0311 L12: -8.7748 REMARK 3 L13: -0.0944 L23: -0.1761 REMARK 3 S TENSOR REMARK 3 S11: 0.2057 S12: 0.4045 S13: -1.0322 REMARK 3 S21: -0.2550 S22: -0.2559 S23: 0.6211 REMARK 3 S31: -0.0839 S32: -0.1936 S33: 0.0501 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: ARP/WARP WAS USED IN MAP IMPROVEMENT REMARK 3 MODE. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL REMARK 3 GEOMETRY WAS ASSESSED ON THE MOLPROBITY SERVER. REMARK 4 REMARK 4 5W9Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228373. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-13 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 : 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) : 0.979590 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AIMLESS 0.5.32, XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22639 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 33.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.72600 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 REMARK 200 STARTING MODEL: PDB ENTRIES 4HP3, 3QMD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG-400, 0.2 M MAGNESIUM CHLORIDE, REMARK 280 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, 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 69.66950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.66950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.90000 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: 2970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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: 2490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 329 REMARK 465 THR A 330 REMARK 465 ASN A 331 REMARK 465 ARG A 332 REMARK 465 GLY B 329 REMARK 465 THR B 330 REMARK 465 ASN B 331 REMARK 465 ARG B 332 REMARK 465 ARG B 333 REMARK 465 ALA B 340 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 337 NZ REMARK 470 LEU A 345 CG CD1 CD2 REMARK 470 ARG A 347 CG CD NE CZ NH1 NH2 REMARK 470 MET A 348 CG SD CE REMARK 470 GLN A 379 CD OE1 NE2 REMARK 470 SER A 388 OG REMARK 470 GLN B 334 CG CD OE1 NE2 REMARK 470 LEU B 345 CG CD1 CD2 REMARK 470 ARG B 347 CG CD NE CZ NH1 NH2 REMARK 470 MET B 348 CG SD CE REMARK 470 LYS B 368 NZ REMARK 470 GLN B 379 CG CD OE1 NE2 REMARK 470 PHE B 380 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER B 388 OG 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 ASP A 354 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG B 347 -73.67 -62.56 REMARK 500 CYS B 372 131.39 -33.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 338 SG REMARK 620 2 CYS A 341 SG 109.0 REMARK 620 3 CYS A 344 SG 119.7 106.1 REMARK 620 4 CYS A 377 SG 106.7 114.5 100.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 350 SG REMARK 620 2 CYS A 353 SG 109.8 REMARK 620 3 CYS A 356 SG 122.7 104.2 REMARK 620 4 CYS A 372 SG 104.9 113.7 101.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 338 SG REMARK 620 2 CYS B 341 SG 111.2 REMARK 620 3 CYS B 344 SG 120.6 95.0 REMARK 620 4 CYS B 377 SG 102.0 128.9 100.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 350 SG REMARK 620 2 CYS B 353 SG 108.9 REMARK 620 3 CYS B 356 SG 124.5 104.0 REMARK 620 4 CYS B 372 SG 103.7 115.2 100.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1002 DBREF 5W9Q A 330 388 UNP Q9UIS9 MBD1_HUMAN 330 388 DBREF 5W9Q B 330 388 UNP Q9UIS9 MBD1_HUMAN 330 388 DBREF 5W9Q C 1 12 PDB 5W9Q 5W9Q 1 12 DBREF 5W9Q D 1 12 PDB 5W9Q 5W9Q 1 12 DBREF 5W9Q E 1 12 PDB 5W9Q 5W9Q 1 12 DBREF 5W9Q F 1 12 PDB 5W9Q 5W9Q 1 12 SEQADV 5W9Q GLY A 329 UNP Q9UIS9 EXPRESSION TAG SEQADV 5W9Q GLY B 329 UNP Q9UIS9 EXPRESSION TAG SEQRES 1 A 60 GLY THR ASN ARG ARG GLN ASN ARG LYS CYS GLY ALA CYS SEQRES 2 A 60 ALA ALA CYS LEU ARG ARG MET ASP CYS GLY ARG CYS ASP SEQRES 3 A 60 PHE CYS CYS ASP LYS PRO LYS PHE GLY GLY SER ASN GLN SEQRES 4 A 60 LYS ARG GLN LYS CYS ARG TRP ARG GLN CYS LEU GLN PHE SEQRES 5 A 60 ALA MET LYS ARG LEU LEU PRO SER SEQRES 1 B 60 GLY THR ASN ARG ARG GLN ASN ARG LYS CYS GLY ALA CYS SEQRES 2 B 60 ALA ALA CYS LEU ARG ARG MET ASP CYS GLY ARG CYS ASP SEQRES 3 B 60 PHE CYS CYS ASP LYS PRO LYS PHE GLY GLY SER ASN GLN SEQRES 4 B 60 LYS ARG GLN LYS CYS ARG TRP ARG GLN CYS LEU GLN PHE SEQRES 5 B 60 ALA MET LYS ARG LEU LEU PRO SER SEQRES 1 C 12 DG DC DC DA DA DC DG DT DT DG DG DC SEQRES 1 D 12 DG DC DC DA DA DC DG DT DT DG DG DC SEQRES 1 E 12 DG DC DC DA DA DC DG DT DT DG DG DC SEQRES 1 F 12 DG DC DC DA DA DC DG DT DT DG DG DC HET ZN A1001 1 HET ZN A1002 1 HET UNX A1003 1 HET UNX A1004 1 HET UNX A1005 1 HET UNX A1006 1 HET UNX A1007 1 HET UNX A1008 1 HET ZN B1001 1 HET ZN B1002 1 HET UNX B1003 1 HET UNX B1004 1 HET UNX B1005 1 HET UNX B1006 1 HET UNX B1007 1 HET UNX B1008 1 HET UNX B1009 1 HET UNX B1010 1 HET UNX C 101 1 HET UNX D 101 1 HETNAM ZN ZINC ION HETNAM UNX UNKNOWN ATOM OR ION FORMUL 7 ZN 4(ZN 2+) FORMUL 9 UNX 16(X) FORMUL 27 HOH *46(H2 O) HELIX 1 AA1 CYS A 341 ARG A 346 1 6 HELIX 2 AA2 CYS A 353 LYS A 359 1 7 HELIX 3 AA3 PRO A 360 GLY A 363 5 4 HELIX 4 AA4 CYS A 372 GLN A 376 5 5 HELIX 5 AA5 MET A 382 LEU A 386 5 5 HELIX 6 AA6 ALA B 342 ARG B 346 1 5 HELIX 7 AA7 CYS B 353 LYS B 359 1 7 HELIX 8 AA8 PRO B 360 GLY B 363 5 4 HELIX 9 AA9 CYS B 372 GLN B 376 5 5 HELIX 10 AB1 MET B 382 LEU B 386 5 5 LINK SG CYS A 338 ZN ZN A1002 1555 1555 2.29 LINK SG CYS A 341 ZN ZN A1002 1555 1555 2.33 LINK SG CYS A 344 ZN ZN A1002 1555 1555 2.36 LINK SG CYS A 350 ZN ZN A1001 1555 1555 2.31 LINK SG CYS A 353 ZN ZN A1001 1555 1555 2.28 LINK SG CYS A 356 ZN ZN A1001 1555 1555 2.34 LINK SG CYS A 372 ZN ZN A1001 1555 1555 2.28 LINK SG CYS A 377 ZN ZN A1002 1555 1555 2.32 LINK SG CYS B 338 ZN ZN B1002 1555 1555 2.34 LINK SG CYS B 341 ZN ZN B1002 1555 1555 2.32 LINK SG CYS B 344 ZN ZN B1002 1555 1555 2.38 LINK SG CYS B 350 ZN ZN B1001 1555 1555 2.30 LINK SG CYS B 353 ZN ZN B1001 1555 1555 2.30 LINK SG CYS B 356 ZN ZN B1001 1555 1555 2.35 LINK SG CYS B 372 ZN ZN B1001 1555 1555 2.28 LINK SG CYS B 377 ZN ZN B1002 1555 1555 2.34 SITE 1 AC1 5 CYS A 350 GLY A 351 CYS A 353 CYS A 356 SITE 2 AC1 5 CYS A 372 SITE 1 AC2 5 CYS A 338 GLY A 339 CYS A 341 CYS A 344 SITE 2 AC2 5 CYS A 377 SITE 1 AC3 4 CYS B 350 CYS B 353 CYS B 356 CYS B 372 SITE 1 AC4 4 CYS B 338 CYS B 341 CYS B 344 CYS B 377 CRYST1 139.339 27.800 64.914 90.00 106.52 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 0.007177 0.000000 0.002128 0.00000 SCALE2 0.000000 0.035971 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016068 0.00000