Header list of 1d9n.pdb file
Complete list - b 16 2 Bytes
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
MODEL 1
Complete list - b 16 2 Bytes