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- PDB-2b2y: Tandem chromodomains of human CHD1 -

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Basic information

Entry
Database: PDB / ID: 2b2y
TitleTandem chromodomains of human CHD1
Components(Chromodomain-helicase-DNA-binding protein 1) x 2
KeywordsPEPTIDE BINDING PROTEIN / CHD / Chromodomain / three stranded antiparallel Beta sheet / alpha helix linker
Function / homology
Function and homology information


nucleosome organization / ATP-dependent chromatin remodeler activity / histone H3K4me3 reader activity / host-mediated activation of viral transcription / nuclear chromosome / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / histone binding / Estrogen-dependent gene expression / chromatin remodeling ...nucleosome organization / ATP-dependent chromatin remodeler activity / histone H3K4me3 reader activity / host-mediated activation of viral transcription / nuclear chromosome / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / histone binding / Estrogen-dependent gene expression / chromatin remodeling / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain ...CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFlanagan IV, J.F. / Mi, L.-Z. / Chruszcz, M. / Cymborowski, M. / Clines, K.L. / Kim, Y. / Minor, W. / Rastinejad, F. / Khorasanizadeh, S.
CitationJournal: Nature / Year: 2005
Title: Double chromodomains cooperate to recognize the methylated histone H3 tail.
Authors: Flanagan, J.F. / Mi, L.Z. / Chruszcz, M. / Cymborowski, M. / Clines, K.L. / Kim, Y. / Minor, W. / Rastinejad, F. / Khorasanizadeh, S.
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Apr 13, 2022Group: Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ACCORDING TO AUTHORS, THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromodomain-helicase-DNA-binding protein 1
B: Chromodomain-helicase-DNA-binding protein 1
C: Chromodomain-helicase-DNA-binding protein 1


Theoretical massNumber of molelcules
Total (without water)57,9883
Polymers57,9883
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.270, 55.031, 101.550
Angle α, β, γ (deg.)90.00, 112.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chromodomain-helicase-DNA-binding protein 1 / CHD-1


Mass: 22146.762 Da / Num. of mol.: 2 / Fragment: residues 268-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14646
#2: Protein Chromodomain-helicase-DNA-binding protein 1 / CHD-1


Mass: 13694.292 Da / Num. of mol.: 1 / Fragment: residues 268-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14646
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 283 K / pH: 8
Details: 4% PEG3350, 0.05M HEPES, 10mM BTP, pH 8.0, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97928
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2004
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.35→31.3 Å / Num. obs: 21913 / % possible obs: 91.1 % / Redundancy: 3.4 % / Rsym value: 0.088 / Net I/σ(I): 11.6
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.254 / % possible all: 76.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.601data extraction
MAR345data collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B2T without chain D

2b2t


Resolution: 2.35→15 Å / Isotropic thermal model: ISOTROPIC / σ(F): 3580 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1251 5.2 %RANDOM
Rwork0.215 ---
obs0.215 18256 75.8 %-
all-21913 --
Solvent computationBsol: 37.66 Å2
Displacement parametersBiso mean: 46.23 Å2
Baniso -1Baniso -2Baniso -3
1-11.931 Å20 Å21.131 Å2
2---5.364 Å20 Å2
3----6.567 Å2
Refinement stepCycle: LAST / Resolution: 2.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 0 197 3707
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.35→2.43 Å / Total num. of bins used: 10
Num. reflection% reflection
Rwork1720 -
Rfree-5.2 %
obs-76.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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