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- PDB-6k01: Crystal structure of xH2A-H2B -

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Basic information

Entry
Database: PDB / ID: 6k01
TitleCrystal structure of xH2A-H2B
Components
  • Histone H2A
  • Histone H2B 1.1
KeywordsCHAPERONE / H2A / H2B
Function / homology
Function and homology information


structural constituent of chromatin / heterochromatin formation / nucleosome / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A 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 1.1 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.839 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
C: Histone H2A
D: Histone H2B 1.1


Theoretical massNumber of molelcules
Total (without water)21,3142
Polymers21,3142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-44 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.923, 46.923, 67.129
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Histone H2A


Mass: 10133.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q6AZJ8
#2: Protein Histone H2B 1.1 / H2B1.1


Mass: 11179.959 Da / Num. of mol.: 1 / Mutation: S30T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P02281

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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 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 0.1M HEPES pH=7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.839→40.64 Å / Num. obs: 3756 / % possible obs: 99.6 % / Redundancy: 4.4 % / Net I/σ(I): 12.7
Reflection shellResolution: 2.84→2.94 Å / Rmerge(I) obs: 0.831 / Num. unique obs: 3756

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOI

1aoi


Resolution: 2.839→40.637 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 31.85 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2782 375 9.98 %
Rwork0.223 3381 -
obs0.2286 3756 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.82 Å2 / Biso mean: 46.6349 Å2 / Biso min: 21 Å2
Refinement stepCycle: final / Resolution: 2.839→40.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 0 0 1280
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 (%)
2.8394-3.25010.34721180.25831046116489
3.2501-4.09420.2751420.226211511293100
4.0942-40.64070.25641150.208811841299100
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)
13.6307-0.739-0.07794.43130.94532.1156-0.0652-0.12690.19350.16590.147-0.1342-0.26310.0794-0.05140.40270.05080.05250.3005-0.01380.20668.58678.10620.0172
22.4332-1.0805-0.53442.22811.57762.10250.12890.06990.1803-0.03280.0757-0.4403-0.09870.3592-0.14840.33730.01160.01250.26620.01480.341710.28162.523-0.2573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' and resid 23 through 99)C23 - 99
2X-RAY DIFFRACTION2(chain 'D' and resid 31 through 119)D31 - 119

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