HEADER DNA BINDING PROTEIN/DNA 12-APR-18 6D1T TITLE COMPLEX OF MBD1-MBD AND METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-77; 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 (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3'); COMPND 10 CHAIN: B, C; 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28GST-LIC; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS MBD, DNA-METHYLATION, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.LIU,C.XU,W.TEMPEL,C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,J.MIN, AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 23-OCT-24 6D1T 1 REMARK REVDAT 2 04-OCT-23 6D1T 1 REMARK REVDAT 1 09-MAY-18 6D1T 0 JRNL AUTH K.LIU,C.XU,W.TEMPEL,C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS, JRNL AUTH 2 J.MIN,STRUCTURAL GENOMICS CONSORTIUM JRNL TITL COMPLEX OF MBD1-MBD AND METHYLATED DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 6633 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 748 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 471 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3630 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 527 REMARK 3 NUCLEIC ACID ATOMS : 488 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.50000 REMARK 3 B22 (A**2) : -0.77000 REMARK 3 B33 (A**2) : 0.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.355 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.249 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.229 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.837 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1099 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 745 ; 0.002 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1588 ; 1.533 ; 1.518 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1753 ; 0.991 ; 2.189 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 69 ; 6.121 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 23 ;17.132 ;14.348 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 75 ;16.784 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;26.124 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 141 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 935 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 237 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 277 ; 1.416 ; 3.594 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 278 ; 1.414 ; 3.597 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 347 ; 2.294 ; 5.389 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 : 3 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 2 A 70 REMARK 3 ORIGIN FOR THE GROUP (A): -5.5927 -10.5075 24.5611 REMARK 3 T TENSOR REMARK 3 T11: 0.0220 T22: 0.2347 REMARK 3 T33: 0.0262 T12: -0.0317 REMARK 3 T13: -0.0096 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 2.9517 L22: 3.1648 REMARK 3 L33: 8.6906 L12: 1.3640 REMARK 3 L13: -1.6105 L23: -2.2193 REMARK 3 S TENSOR REMARK 3 S11: -0.0220 S12: -0.5089 S13: 0.2307 REMARK 3 S21: 0.0318 S22: 0.1502 S23: 0.2051 REMARK 3 S31: -0.1500 S32: 0.1379 S33: -0.1283 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 12 REMARK 3 ORIGIN FOR THE GROUP (A): -7.5438 -10.8580 9.2748 REMARK 3 T TENSOR REMARK 3 T11: 0.1861 T22: 0.0626 REMARK 3 T33: 0.0137 T12: -0.1065 REMARK 3 T13: -0.0334 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 4.1474 L22: 8.8037 REMARK 3 L33: 1.9058 L12: 1.8120 REMARK 3 L13: -0.6344 L23: 1.3102 REMARK 3 S TENSOR REMARK 3 S11: 0.0712 S12: 0.0342 S13: -0.0748 REMARK 3 S21: 0.1059 S22: -0.0660 S23: 0.1633 REMARK 3 S31: 0.0681 S32: -0.0609 S33: -0.0052 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): -6.2240 -11.4039 8.8767 REMARK 3 T TENSOR REMARK 3 T11: 0.1704 T22: 0.1017 REMARK 3 T33: 0.0180 T12: -0.1218 REMARK 3 T13: -0.0415 T23: 0.0304 REMARK 3 L TENSOR REMARK 3 L11: 3.2976 L22: 11.8766 REMARK 3 L33: 0.4788 L12: 0.4653 REMARK 3 L13: -0.0253 L23: 1.1219 REMARK 3 S TENSOR REMARK 3 S11: 0.0089 S12: 0.0321 S13: -0.0826 REMARK 3 S21: -0.4285 S22: -0.0569 S23: 0.1285 REMARK 3 S31: 0.0091 S32: -0.0243 S33: 0.0480 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: COOT WAS USED FOR INTERACTIVE MODEL REMARK 3 BUILDING. MODEL GEOMETRY WAS ASSESSED WITH PHENIX.MOLPROBITY. REMARK 3 DIFFERENCE DENSITY NEAR GLY54 AND PRO55 SUGGESTS THAT THE LINK REMARK 3 MAY ALTERNATELY BE A CIS OR TRANS PEPTIDE. REMARK 4 REMARK 4 6D1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233720. 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 : 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) : 0.97911 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 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7412 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 46.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 1.08300 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: EARLIER VERSION OF PDB ENTRY 6CC8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG-550-MME, 0.1 M MAGNESIUM REMARK 280 CHLORIDE, 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 69.43600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.43600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 14.28700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.09650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 14.28700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.09650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.43600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 14.28700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.09650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.43600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 14.28700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.09650 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: 4060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 MET A 1 REMARK 465 TYR A 71 REMARK 465 PRO A 72 REMARK 465 ALA A 73 REMARK 465 PRO A 74 REMARK 465 LYS A 75 REMARK 465 ALA A 76 REMARK 465 HIS A 77 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 ASP A 4 OD1 OD2 REMARK 470 LYS A 16 NZ REMARK 470 LYS A 23 CE NZ REMARK 470 ARG A 42 NE CZ NH1 NH2 REMARK 470 LEU A 61 CG CD1 CD2 REMARK 470 GLN A 66 CG CD OE1 NE2 REMARK 470 CYS A 70 CA C O CB SG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DA C 5 O3' 5CM C 6 P -0.078 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 ALA A 56 -51.94 -27.64 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 C 5 and 5CM C 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 C 6 and DG C REMARK 800 7 DBREF 6D1T A 1 77 UNP Q9UIS9 MBD1_HUMAN 1 77 DBREF 6D1T B 1 12 PDB 6D1T 6D1T 1 12 DBREF 6D1T C 1 12 PDB 6D1T 6D1T 1 12 SEQADV 6D1T GLY A -1 UNP Q9UIS9 EXPRESSION TAG SEQADV 6D1T SER A 0 UNP Q9UIS9 EXPRESSION TAG SEQRES 1 A 79 GLY SER MET ALA GLU ASP TRP LEU ASP CYS PRO ALA LEU SEQRES 2 A 79 GLY PRO GLY TRP LYS ARG ARG GLU VAL PHE ARG LYS SER SEQRES 3 A 79 GLY ALA THR CYS GLY ARG SER ASP THR TYR TYR GLN SER SEQRES 4 A 79 PRO THR GLY ASP ARG ILE ARG SER LYS VAL GLU LEU THR SEQRES 5 A 79 ARG TYR LEU GLY PRO ALA CYS ASP LEU THR LEU PHE ASP SEQRES 6 A 79 PHE LYS GLN GLY ILE LEU CYS TYR PRO ALA PRO LYS ALA SEQRES 7 A 79 HIS SEQRES 1 B 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 C 12 DG DC DC DA DA 5CM DG DT DT DG DG DC HET 5CM B 6 20 HET 5CM C 6 20 HET UNX A 101 1 HET UNX A 102 1 HET UNX A 103 1 HET UNX A 104 1 HET UNX A 105 1 HET UNX B 101 1 HET UNX B 102 1 HET UNX B 103 1 HET UNX C 101 1 HET UNX C 102 1 HET UNX C 103 1 HET UNX C 104 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 4 UNX 12(X) HELIX 1 AA1 SER A 45 GLY A 54 1 10 SHEET 1 AA1 4 LEU A 6 ASP A 7 0 SHEET 2 AA1 4 LYS A 16 PHE A 21 -1 O ARG A 17 N LEU A 6 SHEET 3 AA1 4 SER A 31 GLN A 36 -1 O TYR A 34 N ARG A 18 SHEET 4 AA1 4 ARG A 42 ILE A 43 -1 O ILE A 43 N TYR A 35 SSBOND 1 CYS A 57 CYS A 57 1555 3455 2.05 LINK O3' DA B 5 P 5CM B 6 1555 1555 1.62 LINK O3' 5CM B 6 P DG B 7 1555 1555 1.64 LINK O3' DA C 5 P 5CM C 6 1555 1555 1.53 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.60 SITE 1 AC1 9 ARG A 44 SER A 45 LYS A 46 VAL A 47 SITE 2 AC1 9 DG B 7 DT B 8 DT B 9 DA C 4 SITE 3 AC1 9 DG C 7 SITE 1 AC2 8 ARG A 44 SER A 45 VAL A 47 DA B 5 SITE 2 AC2 8 5CM B 6 DG B 7 DA C 5 DT C 8 CRYST1 28.574 74.193 138.872 90.00 90.00 90.00 C 2 2 21 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 0.034997 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013478 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007201 0.00000