[English] 日本語
Yorodumi
- PDB-2xb0: DNA-binding domain from Saccharomyces cerevisiae chromatin- remod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xb0
TitleDNA-binding domain from Saccharomyces cerevisiae chromatin- remodelling protein Chd1
ComponentsCHROMO DOMAIN-CONTAINING PROTEIN 1
KeywordsHYDROLASE / DNA-BINDING PROTEIN / TRANSCRIPTION / CHROMATIN REGULATOR
Function / homology
Function and homology information


nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / nucleosome organization / SLIK (SAGA-like) complex / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / SAGA complex ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / nucleosome organization / SLIK (SAGA-like) complex / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / SAGA complex / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / methylated histone binding / helicase activity / transcription elongation by RNA polymerase II / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / histone binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus
Similarity search - Function
Helix Hairpins - #1440 / Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain ...Helix Hairpins - #1440 / Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Helix Hairpins / Homeodomain-like / Helix non-globular / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / Special / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chromo domain-containing protein 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsRyan, D.P. / Sundaramoorthy, R. / Owen-Hughes, T.
CitationJournal: Embo J. / Year: 2011
Title: The DNA-Binding Domain of the Chd1 Chromatin- Remodelling Enzyme Contains Sant and Slide Domains.
Authors: Ryan, D.P. / Sundaramoorthy, R. / Martin, D. / Singh, V. / Owen-Hughes, T.
History
DepositionApr 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Database references / Version format compliance
Revision 1.2Mar 6, 2013Group: Data collection / Non-polymer description / Other
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: CHROMO DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5705
Polymers30,3151
Non-polymers2554
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.450, 91.120, 98.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CHROMO DOMAIN-CONTAINING PROTEIN 1 / ATP-DEPENDENT HELICASE CHD1 / CHD1


Mass: 30314.662 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN, RESIDUES 1009-1274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PGEX-6P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS
References: UniProt: P32657, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPARTIAL SEQUENCE (AA 1009-1274) CORRESPONDING TO THE DNA- BINDING DOMAIN OF YEAST CHD1. FIRST FOUR ...PARTIAL SEQUENCE (AA 1009-1274) CORRESPONDING TO THE DNA- BINDING DOMAIN OF YEAST CHD1. FIRST FOUR RESIDUES (GPLG) ARE NON-NATIVE AND ARE LEFT FROM CLEAVAGE OF THE GST-TAG WITH PRESCISSION PROTEASE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.57 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M TRIS, PH 8.5, 28% PEG 4K, 0.35 M MGCL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9775
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 11, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 2→49.2 Å / Num. obs: 22943 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Biso Wilson estimate: 34.64 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.5 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→49.255 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
Details: RIDING HYDROGENS WERE USED IN REFINEMENT AMINO ACIDS 209-240 (NEVHNPVAKKSASSSDTTPTPSKKGKGITGSS) AND 266-270 (TKSPS) ARE DISORDERED WERE NOT MODELLED OWING TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2479 2263 9.9 %
Rwork0.205 --
obs0.2093 22894 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.114 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 61.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.8428 Å20 Å20 Å2
2--5.0238 Å20 Å2
3----6.8666 Å2
Refinement stepCycle: LAST / Resolution: 2→49.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 14 109 1965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181938
X-RAY DIFFRACTIONf_angle_d1.3592598
X-RAY DIFFRACTIONf_dihedral_angle_d14.263752
X-RAY DIFFRACTIONf_chiral_restr0.085279
X-RAY DIFFRACTIONf_plane_restr0.005330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.35912080.3271989X-RAY DIFFRACTION95
2.0715-2.15440.30082080.28382026X-RAY DIFFRACTION98
2.1544-2.25250.30872100.24132029X-RAY DIFFRACTION96
2.2525-2.37130.28172330.21262002X-RAY DIFFRACTION96
2.3713-2.51980.25632060.19842062X-RAY DIFFRACTION97
2.5198-2.71440.25832480.19612021X-RAY DIFFRACTION98
2.7144-2.98750.26762280.20912084X-RAY DIFFRACTION98
2.9875-3.41970.26622460.21732072X-RAY DIFFRACTION98
3.4197-4.30810.23232340.17542120X-RAY DIFFRACTION99
4.3081-49.26990.19952420.18662226X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.51340.2610.4042.40282.03321.824-0.0189-0.1516-0.01880.74280.1675-0.25860.330.2885-0.13680.4699-0.0347-0.08930.3210.03240.251210.675665.306379.2636
22.39431.5120.90813.26750.09640.8162-0.28210.2469-0.0041-1.05540.3969-0.06050.11430.0501-0.08290.8428-0.0351-0.04120.3014-0.00890.2257-10.674434.271755.7702
32.34220.17272.36810.7181.50195.15440.2534-0.1417-0.72850.0753-0.6913-0.14260.8482-0.05860.11620.6494-0.1447-0.05060.36810.11010.3873-1.284752.386374.4755
41.98850.95470.30681.39340.82261.84990.0822-0.12460.6320.0012-0.17030.0882-0.0359-0.22460.14050.0630.0027-0.00730.1728-0.10030.271-1.83175.637258.5856
50.91920.7220.55780.63960.44020.4060.3516-1.47810.98280.3615-0.83650.49290.1704-0.77680.43990.1251-0.1660.09860.8782-0.43240.5123-15.49475.115866.0314
61.64541.1824-1.53092.25340.64363.70660.1182-0.1278-0.16520.3804-0.3762-0.23470.6517-0.84180.20.1906-0.1045-0.00730.2784-0.03360.2942-4.326663.97956.8805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN X AND RESID 1:60)
2X-RAY DIFFRACTION2(CHAIN X AND RESID 61:108)
3X-RAY DIFFRACTION3(CHAIN X AND RESID 109:128)
4X-RAY DIFFRACTION4(CHAIN X AND RESID 129:205)
5X-RAY DIFFRACTION5(CHAIN X AND RESID 206:250)
6X-RAY DIFFRACTION6(CHAIN X AND RESID 251:266)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more