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- PDB-6k03: Crystal structure of ceH2A-H2B -

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Basic information

Entry
Database: PDB / ID: 6k03
TitleCrystal structure of ceH2A-H2B
ComponentsHistone H2B 1,Histone H2A
KeywordsCHAPERONE / H2A-H2B
Function / homology
Function and homology information


Negative Regulation of CDH1 Gene Transcription / Metalloprotease DUBs / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / : / : / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / : ...Negative Regulation of CDH1 Gene Transcription / Metalloprotease DUBs / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / : / : / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / : / Condensation of Prophase Chromosomes / Ub-specific processing proteases / structural constituent of chromatin / heterochromatin formation / nucleosome / defense response to Gram-negative bacterium / protein heterodimerization activity / innate immune response / DNA repair / regulation of DNA-templated transcription / chromatin / protein-containing complex binding / DNA binding / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2B 1 / Histone H2A
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.857 Å
AuthorsLiu, Y.R.
CitationJournal: Structure / Year: 2019
Title: Crystal structure of xlH2A-H2B
Authors: Liu, Y.R.
History
DepositionMay 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Histone H2B 1,Histone H2A


Theoretical massNumber of molelcules
Total (without water)22,6531
Polymers22,6531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9110 Å2
Unit cell
Length a, b, c (Å)63.839, 63.839, 70.032
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Histone H2B 1,Histone H2A


Mass: 22653.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P04255, UniProt: P09588

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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: 1.82 Å3/Da / Density % sol: 32.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.857→44.39 Å / Num. obs: 3967 / % possible obs: 97.5 % / Redundancy: 5.4 % / Net I/σ(I): 12.15
Reflection shellResolution: 2.857→2.96 Å / Rmerge(I) obs: 0.68 / Num. unique obs: 3967

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K01

6k01


Resolution: 2.857→43.394 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 29.74
RfactorNum. reflection% reflection
Rfree0.2837 403 10.18 %
Rwork0.231 --
obs0.2366 3959 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.41 Å2 / Biso mean: 50.6172 Å2 / Biso min: 27.77 Å2
Refinement stepCycle: final / Resolution: 2.857→43.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 0 0 1281
Num. residues----166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8569-3.27020.36771190.30251168128797
3.2702-4.11960.31541350.23211177131298
4.1196-43.39880.24371490.20561211136097
Refinement TLS params.Method: refined / Origin x: -19.7115 Å / Origin y: 13.1587 Å / Origin z: 1.9542 Å
111213212223313233
T0.3384 Å2-0.006 Å2-0.013 Å2-0.3492 Å20.0015 Å2--0.3474 Å2
L2.3239 °2-0.0593 °2-0.794 °2-1.306 °20.3684 °2--2.1932 °2
S-0.0072 Å °-0.1981 Å °-0.1744 Å °0.0678 Å °-0.0304 Å °0.0984 Å °-0.1377 Å °-0.0328 Å °0.0207 Å °
Refinement TLS groupSelection details: (chain 'D' and resid 30 through 212)

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