PDB Short entry for 1D9N HEADER GENE REGULATION 28-OCT-99 1D9N TITLE SOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE TITLE 2 METHYLATION-DEPENDENT TRANSCRIPTIONAL REPRESSOR MBD1/PCM1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING PROTEIN MBD1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: METHYL-CPG-BINDING DOMAIN OF MBD1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5A; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS MBD, METHYL-CPG, PCM1, METHYLATION, DNA BINDING DOMAIN, GENE KEYWDS 2 REGULATION EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR I.OHKI,N.SHIMOTAKE,N.FUJITA,M.NAKAO,M.SHIRAKAWA REVDAT 3 16-FEB-22 1D9N 1 REMARK REVDAT 2 24-FEB-09 1D9N 1 VERSN REVDAT 1 28-OCT-00 1D9N 0 JRNL AUTH I.OHKI,N.SHIMOTAKE,N.FUJITA,M.NAKAO,M.SHIRAKAWA JRNL TITL SOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE JRNL TITL 2 METHYLATION-DEPENDENT TRANSCRIPTIONAL REPRESSOR MBD1. JRNL REF EMBO J. V. 18 6653 1999 JRNL REFN ISSN 0261-4189 JRNL PMID 10581239 JRNL DOI 10.1093/EMBOJ/18.23.6653 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.H.CROSS,R.R.MEEHAN,X.NAN,A.BIRD REMARK 1 TITL A COMPONENT OF THE TRANSCRIPTIONAL REPRESSOR MECP1 SHARES A REMARK 1 TITL 2 MOTIF WITH DNA METHYLTRANSFERASE AND HRX PROTEINS REMARK 1 REF NAT.GENET. V. 16 256 1997 REMARK 1 REFN ISSN 1061-4036 REMARK 1 REFERENCE 2 REMARK 1 AUTH N.FUJITA,S.TAKEBAYASHI,K.OKUMURA,S.KUDO,T.CHIBA,H.SAYA, REMARK 1 AUTH 2 M.NAKAO REMARK 1 TITL METHYLATION-MEDIATED TRANSCRIPTIONAL SILENCING IN REMARK 1 TITL 2 EUCHROMATIN BY METHYL-CPG BINDING PROTEIN MBD1 ISOFORMS REMARK 1 REF MOL.CELL.BIOL. V. 19 6415 1999 REMARK 1 REFN ISSN 0270-7306 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 1.7, X-PLOR 3.8 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1270 NOE CONSTRAINTS, 44 REMARK 3 DIHEDRAL ANGLE REMARK 3 CONSTRAINTS AND 15 HYDROGEN BONDS. REMARK 4 REMARK 4 1D9N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000009917. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50MM KCL REMARK 210 PRESSURE : 1 ATMOSPHERE REMARK 210 SAMPLE CONTENTS : 1.3MM MBD U-15N,13C; 20MM REMARK 210 PHOSPHATE BUFFER; 50MM KCL; 5MM REMARK 210 DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 4D_13C/13C- REMARK 210 SEPARATED_NOESY; 4D_13C/15N- REMARK 210 SEPARATED_NOESY; HMQC-J REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP 97NOV REMARK 210 METHOD USED : STRUCTURE CALCULATIONS WERE REMARK 210 PERFORMED FOLLOWING SIMULATED REMARK 210 ANNEALING PROTOCOLS USING X-PLOR REMARK 210 3.8. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 125 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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: REMARK 210 THE STRUCTURE WAS DETERMINED USING MULTI-DIMENSIONAL HETERONUCLEAR REMARK 210 NMR REMARK 210 SPECTROSCOPY. 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 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 ALA A 2 -175.54 176.54 REMARK 500 1 GLU A 3 -92.16 -127.67 REMARK 500 1 TRP A 5 94.55 -54.68 REMARK 500 1 PHE A 21 27.95 48.59 REMARK 500 1 LYS A 23 -83.92 -79.67 REMARK 500 1 ALA A 26 172.55 -53.92 REMARK 500 1 LYS A 46 -94.09 62.73 REMARK 500 1 LEU A 59 12.09 -143.71 REMARK 500 1 LYS A 65 -40.46 -179.52 REMARK 500 1 ALA A 73 91.24 48.22 REMARK 500 2 GLU A 3 -71.63 -97.66 REMARK 500 2 ASP A 4 27.12 -148.06 REMARK 500 2 TRP A 5 92.24 -49.54 REMARK 500 2 PHE A 21 16.36 56.57 REMARK 500 2 LYS A 23 -76.26 -119.79 REMARK 500 2 SER A 24 -70.89 63.20 REMARK 500 2 ALA A 26 -159.11 -76.16 REMARK 500 2 CYS A 28 64.64 -158.18 REMARK 500 2 SER A 31 123.52 63.81 REMARK 500 2 LEU A 59 12.04 -146.35 REMARK 500 2 PHE A 64 63.00 -66.94 REMARK 500 2 LYS A 65 -43.70 -179.65 REMARK 500 2 PRO A 72 -161.02 -77.71 REMARK 500 2 ALA A 73 78.73 56.79 REMARK 500 3 GLU A 3 -147.25 -92.69 REMARK 500 3 ASP A 4 40.38 -104.45 REMARK 500 3 TRP A 5 104.89 -57.88 REMARK 500 3 LEU A 11 -61.34 -101.15 REMARK 500 3 ARG A 22 -79.80 60.68 REMARK 500 3 THR A 27 -46.16 -134.05 REMARK 500 3 ARG A 30 153.99 65.07 REMARK 500 3 SER A 31 133.01 -177.77 REMARK 500 3 LYS A 46 -71.84 -68.96 REMARK 500 3 PHE A 64 61.33 -69.98 REMARK 500 3 LYS A 65 -37.37 -174.46 REMARK 500 3 PRO A 72 -159.67 -77.75 REMARK 500 3 ALA A 73 -52.97 164.07 REMARK 500 4 ALA A 2 178.10 -54.72 REMARK 500 4 ASP A 4 67.86 -150.63 REMARK 500 4 TRP A 5 102.73 -44.14 REMARK 500 4 LEU A 11 -61.99 -94.13 REMARK 500 4 ALA A 26 -71.45 -69.77 REMARK 500 4 CYS A 28 -76.98 -46.09 REMARK 500 4 SER A 31 175.01 65.86 REMARK 500 4 ARG A 44 18.17 -160.31 REMARK 500 4 LYS A 46 -92.49 64.36 REMARK 500 4 THR A 50 -70.87 -65.65 REMARK 500 4 PHE A 64 65.04 -67.19 REMARK 500 4 LYS A 65 -37.90 171.48 REMARK 500 5 ASP A 4 55.98 -102.85 REMARK 500 REMARK 500 THIS ENTRY HAS 290 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 17 0.11 SIDE CHAIN REMARK 500 1 ARG A 18 0.14 SIDE CHAIN REMARK 500 1 ARG A 22 0.27 SIDE CHAIN REMARK 500 1 ARG A 30 0.25 SIDE CHAIN REMARK 500 1 ARG A 42 0.18 SIDE CHAIN REMARK 500 1 ARG A 51 0.21 SIDE CHAIN REMARK 500 2 ARG A 17 0.32 SIDE CHAIN REMARK 500 2 ARG A 18 0.19 SIDE CHAIN REMARK 500 2 ARG A 22 0.20 SIDE CHAIN REMARK 500 2 ARG A 30 0.29 SIDE CHAIN REMARK 500 2 ARG A 42 0.23 SIDE CHAIN REMARK 500 2 ARG A 44 0.32 SIDE CHAIN REMARK 500 2 ARG A 51 0.31 SIDE CHAIN REMARK 500 3 ARG A 18 0.30 SIDE CHAIN REMARK 500 3 ARG A 30 0.32 SIDE CHAIN REMARK 500 3 ARG A 42 0.24 SIDE CHAIN REMARK 500 3 ARG A 44 0.32 SIDE CHAIN REMARK 500 3 ARG A 51 0.10 SIDE CHAIN REMARK 500 4 ARG A 17 0.27 SIDE CHAIN REMARK 500 4 ARG A 18 0.12 SIDE CHAIN REMARK 500 4 ARG A 22 0.30 SIDE CHAIN REMARK 500 4 ARG A 30 0.32 SIDE CHAIN REMARK 500 4 ARG A 42 0.28 SIDE CHAIN REMARK 500 4 ARG A 44 0.30 SIDE CHAIN REMARK 500 5 ARG A 17 0.15 SIDE CHAIN REMARK 500 5 ARG A 18 0.14 SIDE CHAIN REMARK 500 5 ARG A 22 0.30 SIDE CHAIN REMARK 500 5 ARG A 30 0.31 SIDE CHAIN REMARK 500 5 ARG A 42 0.32 SIDE CHAIN REMARK 500 5 ARG A 44 0.31 SIDE CHAIN REMARK 500 5 ARG A 51 0.28 SIDE CHAIN REMARK 500 6 ARG A 17 0.21 SIDE CHAIN REMARK 500 6 ARG A 30 0.31 SIDE CHAIN REMARK 500 6 ARG A 42 0.28 SIDE CHAIN REMARK 500 6 ARG A 44 0.31 SIDE CHAIN REMARK 500 6 ARG A 51 0.26 SIDE CHAIN REMARK 500 7 ARG A 17 0.31 SIDE CHAIN REMARK 500 7 ARG A 18 0.32 SIDE CHAIN REMARK 500 7 ARG A 22 0.32 SIDE CHAIN REMARK 500 7 ARG A 42 0.26 SIDE CHAIN REMARK 500 7 ARG A 44 0.30 SIDE CHAIN REMARK 500 7 ARG A 51 0.18 SIDE CHAIN REMARK 500 8 ARG A 18 0.31 SIDE CHAIN REMARK 500 8 ARG A 22 0.18 SIDE CHAIN REMARK 500 8 ARG A 30 0.17 SIDE CHAIN REMARK 500 8 ARG A 42 0.20 SIDE CHAIN REMARK 500 8 ARG A 44 0.30 SIDE CHAIN REMARK 500 8 ARG A 51 0.17 SIDE CHAIN REMARK 500 9 ARG A 18 0.22 SIDE CHAIN REMARK 500 9 ARG A 22 0.24 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 155 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1D9N A 1 75 UNP Q9UIS9 MBD1_HUMAN 1 75 SEQRES 1 A 75 MET ALA GLU ASP TRP LEU ASP CYS PRO ALA LEU GLY PRO SEQRES 2 A 75 GLY TRP LYS ARG ARG GLU VAL PHE ARG LYS SER GLY ALA SEQRES 3 A 75 THR CYS GLY ARG SER ASP THR TYR TYR GLN SER PRO THR SEQRES 4 A 75 GLY ASP ARG ILE ARG SER LYS VAL GLU LEU THR ARG TYR SEQRES 5 A 75 LEU GLY PRO ALA CYS ASP LEU THR LEU PHE ASP PHE LYS SEQRES 6 A 75 GLN GLY ILE LEU CYS TYR PRO ALA PRO LYS HELIX 1 1 LYS A 46 GLY A 54 1 9 SHEET 1 A 4 LEU A 6 ASP A 7 0 SHEET 2 A 4 LYS A 16 GLU A 19 -1 N ARG A 17 O LEU A 6 SHEET 3 A 4 THR A 33 GLN A 36 -1 O TYR A 34 N ARG A 18 SHEET 4 A 4 ARG A 42 ILE A 43 -1 O ILE A 43 N TYR A 35 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