HEADER HYDROLASE/DNA 24-APR-14 2MOE TITLE SOLUTION STRUCTURE OF MBD4 METHYL-CYTOSINE BINDING DOMAIN BOUND TO TITLE 2 METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 80-148; COMPND 5 SYNONYM: METHYL-CPG-BINDING ENDONUCLEASE 1, METHYL-CPG-BINDING COMPND 6 PROTEIN MBD4, MISMATCH-SPECIFIC DNA N-GLYCOSYLASE; COMPND 7 EC: 3.2.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*GP*AP*TP*(5CM)P*GP*GP*CP*TP*C)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: MBD4MBD; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*GP*AP*GP*CP*(5CM)P*GP*AP*TP*CP*C)-3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: DNAREV SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MBD4, MED1; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 MOL_ID: 3; SOURCE 9 SYNTHETIC: YES KEYWDS PROTEIN/DNA, METHYLATED DNA, HYDROLASE-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.C.WILLIAMS,N.M.WALAVALKAR REVDAT 3 14-JUN-23 2MOE 1 REMARK SEQADV LINK REVDAT 2 19-NOV-14 2MOE 1 JRNL REVDAT 1 10-SEP-14 2MOE 0 JRNL AUTH N.M.WALAVALKAR,J.M.CRAMER,W.A.BUCHWALD,J.N.SCARSDALE, JRNL AUTH 2 D.C.WILLIAMS JRNL TITL SOLUTION STRUCTURE AND INTRAMOLECULAR EXCHANGE OF JRNL TITL 2 METHYL-CYTOSINE BINDING DOMAIN PROTEIN 4 (MBD4) ON DNA JRNL TITL 3 SUGGESTS A MECHANISM TO SCAN FOR MCPG/TPG MISMATCHES. JRNL REF NUCLEIC ACIDS RES. V. 42 11218 2015 JRNL REFN ISSN 0305-1048 JRNL PMID 25183517 JRNL DOI 10.1093/NAR/GKU782 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MOE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000103857. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2-1.0 MM [U-99% 13C; U-99% REMARK 210 15N] MBD4MBD, 0.2-1.0 MM DNAFOR, REMARK 210 0.2-1.0 MM DNAREV, 90% H2O/10% REMARK 210 D2O; 0.2-1.0 MM [U-13C; U-15N; U- REMARK 210 2H] MBD4MBD, 0.2-1.0 MM DNAFOR, REMARK 210 0.2-1.0 MM DNAREV, 12 MG/ML PF1 REMARK 210 PHAGE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D CBCA(CO)NH; 3D HNCACB; REMARK 210 3D HBHA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR 2.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 LYS A 148 O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 3 DT C 218 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 6 DT C 218 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 13 DT B 204 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 14 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 14 DT C 218 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 18 DT B 204 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 18 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 19 DT C 218 C6 - C5 - C7 ANGL. DEV. = -3.6 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 1 GLU A 81 -164.34 -106.51 REMARK 500 1 ARG A 83 -162.96 -55.54 REMARK 500 1 SER A 85 -9.21 -177.20 REMARK 500 1 LEU A 98 -96.66 -60.51 REMARK 500 1 ALA A 103 111.38 -29.39 REMARK 500 1 SER A 112 167.32 -43.34 REMARK 500 1 ARG A 119 11.76 -146.00 REMARK 500 1 SER A 147 123.02 61.68 REMARK 500 2 SER A 79 -44.35 73.97 REMARK 500 2 GLU A 81 81.49 -176.33 REMARK 500 2 CYS A 82 -150.34 64.79 REMARK 500 2 ARG A 83 6.75 54.68 REMARK 500 2 SER A 85 -36.50 -165.92 REMARK 500 2 ALA A 103 105.94 -32.06 REMARK 500 2 PHE A 143 173.97 -47.14 REMARK 500 3 CYS A 82 76.07 37.64 REMARK 500 3 SER A 85 -92.52 175.38 REMARK 500 3 LEU A 98 -104.77 -68.91 REMARK 500 3 ALA A 103 127.01 -35.29 REMARK 500 3 SER A 147 -124.99 35.05 REMARK 500 4 GLU A 81 -164.55 57.00 REMARK 500 4 CYS A 82 71.15 66.20 REMARK 500 4 SER A 85 -19.54 74.97 REMARK 500 4 PHE A 99 -98.40 -131.99 REMARK 500 4 ALA A 103 131.38 -29.15 REMARK 500 4 SER A 147 -87.91 -124.43 REMARK 500 5 SER A 79 -44.93 -131.98 REMARK 500 5 CYS A 82 5.44 -168.41 REMARK 500 5 ARG A 83 -61.79 -100.18 REMARK 500 5 LYS A 84 15.04 54.03 REMARK 500 5 VAL A 86 72.53 40.69 REMARK 500 5 THR A 144 -179.82 -178.07 REMARK 500 5 LEU A 146 92.86 -50.90 REMARK 500 5 SER A 147 51.84 -171.02 REMARK 500 6 THR A 80 -148.25 50.25 REMARK 500 6 GLU A 81 -79.39 57.26 REMARK 500 6 CYS A 82 -160.49 52.92 REMARK 500 6 SER A 85 -99.44 173.13 REMARK 500 6 ALA A 103 151.99 -36.96 REMARK 500 6 ARG A 119 22.19 -150.35 REMARK 500 6 GLU A 133 -71.94 -90.41 REMARK 500 6 THR A 134 -8.38 61.87 REMARK 500 6 SER A 147 -45.96 -150.53 REMARK 500 7 CYS A 82 -108.02 -156.00 REMARK 500 7 LYS A 84 134.66 72.33 REMARK 500 7 SER A 85 -19.38 72.74 REMARK 500 7 LEU A 98 -107.33 -82.11 REMARK 500 7 ALA A 103 161.96 -37.59 REMARK 500 7 SER A 135 24.66 -76.90 REMARK 500 7 LEU A 146 148.09 -177.08 REMARK 500 REMARK 500 THIS ENTRY HAS 143 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19939 RELATED DB: BMRB DBREF 2MOE A 80 148 UNP O95243 MBD4_HUMAN 80 148 DBREF 2MOE B 201 210 PDB 2MOE 2MOE 201 210 DBREF 2MOE C 211 220 PDB 2MOE 2MOE 211 220 SEQADV 2MOE GLY A 78 UNP O95243 EXPRESSION TAG SEQADV 2MOE SER A 79 UNP O95243 EXPRESSION TAG SEQRES 1 A 71 GLY SER THR GLU CYS ARG LYS SER VAL PRO CYS GLY TRP SEQRES 2 A 71 GLU ARG VAL VAL LYS GLN ARG LEU PHE GLY LYS THR ALA SEQRES 3 A 71 GLY ARG PHE ASP VAL TYR PHE ILE SER PRO GLN GLY LEU SEQRES 4 A 71 LYS PHE ARG SER LYS SER SER LEU ALA ASN TYR LEU HIS SEQRES 5 A 71 LYS ASN GLY GLU THR SER LEU LYS PRO GLU ASP PHE ASP SEQRES 6 A 71 PHE THR VAL LEU SER LYS SEQRES 1 B 10 DG DG DA DT 5CM DG DG DC DT DC SEQRES 1 C 10 DG DA DG DC 5CM DG DA DT DC DC MODRES 2MOE 5CM B 205 DC MODRES 2MOE 5CM C 215 DC HET 5CM B 205 33 HET 5CM C 215 33 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 2 5CM 2(C10 H16 N3 O7 P) HELIX 1 1 SER A 120 GLY A 132 1 13 SHEET 1 A 3 GLU A 91 GLN A 96 0 SHEET 2 A 3 PHE A 106 ILE A 111 -1 O TYR A 109 N VAL A 93 SHEET 3 A 3 LYS A 117 PHE A 118 -1 O PHE A 118 N PHE A 110 LINK O3' DT B 204 P 5CM B 205 1555 1555 1.61 LINK O3' 5CM B 205 P DG B 206 1555 1555 1.61 LINK O3' DC C 214 P 5CM C 215 1555 1555 1.61 LINK O3' 5CM C 215 P DG C 216 1555 1555 1.61 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1