HEADER TRANSCRIPTION 26-JUL-13 2MB7 TITLE SOLUTION STRUCTURE OF MBD3 METHYLCYTOSINE BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: METHYL-CPG-BINDING DOMAIN (UNP RESIDUES 1-70); COMPND 5 SYNONYM: METHYL-CPG-BINDING PROTEIN MBD3; COMPND 6 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS MBD3, DNA METHYLATION, NURD, CHROMATIN, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.C.WILLIAMS JR.,J.N.SCARSDALE REVDAT 4 14-JUN-23 2MB7 1 REMARK SEQADV REVDAT 3 05-FEB-14 2MB7 1 JRNL REVDAT 2 01-JAN-14 2MB7 1 JRNL REVDAT 1 11-DEC-13 2MB7 0 JRNL AUTH J.M.CRAMER,J.N.SCARSDALE,N.M.WALAVALKAR,W.A.BUCHWALD, JRNL AUTH 2 G.D.GINDER,D.C.WILLIAMS JRNL TITL PROBING THE DYNAMIC DISTRIBUTION OF BOUND STATES FOR JRNL TITL 2 METHYLCYTOSINE-BINDING DOMAINS ON DNA. JRNL REF J.BIOL.CHEM. V. 289 1294 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24307175 JRNL DOI 10.1074/JBC.M113.512236 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MB7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000103433. 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 : 0.5-1.0 MM [U-99% 13C; U-99% REMARK 210 15N] MBD3, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC 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 : NMRPIPE, CCPN 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 LEU A 72 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: 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 ARG A 25 35.20 -152.54 REMARK 500 1 SER A 29 16.38 -69.73 REMARK 500 1 MET A 59 173.38 179.50 REMARK 500 2 PRO A 14 155.75 -49.72 REMARK 500 2 ALA A 30 170.39 -44.03 REMARK 500 3 SER A 2 90.34 48.10 REMARK 500 3 ARG A 5 75.15 60.87 REMARK 500 3 SER A 26 164.48 55.78 REMARK 500 3 LEU A 28 -0.51 -58.03 REMARK 500 4 SER A 2 -65.02 -125.47 REMARK 500 4 ARG A 5 178.65 -51.73 REMARK 500 4 SER A 29 22.55 -76.08 REMARK 500 4 ARG A 46 -72.54 -124.58 REMARK 500 4 SER A 47 130.41 -21.26 REMARK 500 5 ARG A 5 106.61 54.02 REMARK 500 5 ALA A 30 155.21 -34.92 REMARK 500 6 ARG A 25 -33.82 -135.01 REMARK 500 6 ALA A 30 131.37 -38.94 REMARK 500 6 MET A 59 126.88 169.45 REMARK 500 6 THR A 63 35.14 -94.71 REMARK 500 7 SER A 2 93.32 50.24 REMARK 500 7 ARG A 5 110.90 55.17 REMARK 500 7 GLN A 15 106.80 -49.93 REMARK 500 7 ARG A 24 90.13 -57.38 REMARK 500 7 ARG A 25 -75.18 -56.25 REMARK 500 7 SER A 26 58.57 -162.37 REMARK 500 7 ALA A 30 170.62 -42.76 REMARK 500 7 HIS A 32 -146.06 -133.11 REMARK 500 8 ALA A 30 152.64 -34.22 REMARK 500 9 SER A 2 -29.06 67.16 REMARK 500 9 ARG A 25 -31.44 -144.53 REMARK 500 9 SER A 29 26.33 -77.27 REMARK 500 9 ALA A 30 150.71 -33.01 REMARK 500 9 MET A 59 171.25 178.10 REMARK 500 9 THR A 63 49.65 -95.35 REMARK 500 10 GLN A 15 107.17 -44.64 REMARK 500 10 SER A 26 -94.54 -34.41 REMARK 500 10 ALA A 30 132.58 -39.07 REMARK 500 10 HIS A 32 102.10 -57.29 REMARK 500 11 SER A 2 -72.46 -65.90 REMARK 500 11 ARG A 5 105.53 60.13 REMARK 500 11 LEU A 13 157.49 -40.70 REMARK 500 11 ARG A 25 19.18 -167.27 REMARK 500 11 SER A 26 -43.40 -149.37 REMARK 500 11 ALA A 30 169.68 -42.39 REMARK 500 11 ARG A 46 -66.71 -130.77 REMARK 500 11 SER A 47 125.91 -15.82 REMARK 500 12 SER A 2 103.31 51.33 REMARK 500 12 GLU A 4 -157.52 -142.99 REMARK 500 12 ARG A 25 -9.20 -170.33 REMARK 500 REMARK 500 THIS ENTRY HAS 81 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19391 RELATED DB: BMRB DBREF 2MB7 A 3 72 UNP O95983 MBD3_HUMAN 1 70 SEQADV 2MB7 GLY A 1 UNP O95983 EXPRESSION TAG SEQADV 2MB7 SER A 2 UNP O95983 EXPRESSION TAG SEQRES 1 A 72 GLY SER MET GLU ARG LYS ARG TRP GLU CYS PRO ALA LEU SEQRES 2 A 72 PRO GLN GLY TRP GLU ARG GLU GLU VAL PRO ARG ARG SER SEQRES 3 A 72 GLY LEU SER ALA GLY HIS ARG ASP VAL PHE TYR TYR SER SEQRES 4 A 72 PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU ALA SEQRES 5 A 72 ARG TYR LEU GLY GLY SER MET ASP LEU SER THR PHE ASP SEQRES 6 A 72 PHE ARG THR GLY LYS MET LEU HELIX 1 1 SER A 47 GLY A 56 1 10 SHEET 1 A 4 TRP A 8 GLU A 9 0 SHEET 2 A 4 GLU A 18 SER A 26 -1 O ARG A 19 N TRP A 8 SHEET 3 A 4 SER A 29 TYR A 38 -1 O HIS A 32 N ARG A 24 SHEET 4 A 4 LYS A 44 PHE A 45 -1 O PHE A 45 N TYR A 37 SHEET 1 B 2 PHE A 64 ASP A 65 0 SHEET 2 B 2 LYS A 70 MET A 71 -1 O LYS A 70 N ASP A 65 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