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- PDB-6w4l: The crystal structure of a single chain H2B-H2A histone chimera f... -

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Basic information

Entry
Database: PDB / ID: 6w4l
TitleThe crystal structure of a single chain H2B-H2A histone chimera from Xenopus laevis
ComponentsHistone H2B 1.1,Histone H2A type 1
KeywordsGENE REGULATION / histone / chromatin
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PYROPHOSPHATE / Histone H2B 1.1 / Histone H2A type 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsWarren, C. / Bonanno, J.B. / Almo, S.C. / Shechter, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135614 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structure of a single-chain H2A/H2B dimer.
Authors: Warren, C. / Bonanno, J.B. / Almo, S.C. / Shechter, D.
History
DepositionMar 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
A: Histone H2B 1.1,Histone H2A type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7002
Polymers20,5221
Non-polymers1781
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.793, 44.679, 66.450
Angle α, β, γ (deg.)90.000, 117.270, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1311-

HOH

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Components

#1: Protein Histone H2B 1.1,Histone H2A type 1 / H2B1.1


Mass: 20521.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: single chain construct linking H2B (aa 34-126) and H2A (aa 14-105); one N-terminal Gly cloning artifact.,single chain construct linking H2B (aa 34-126) and H2A (aa 14-105); one N-terminal Gly cloning artifact.
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: modified pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P02281, UniProt: P06897
#2: Chemical ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.09 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.9 / Details: 0.2M sodium thiocyanate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2017
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.31→26.71 Å / Num. obs: 38073 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.31-1.393.60.8921978654870.6190.551.0521.199.8
4.16-26.713.50.022396311340.9990.0140.02613.989.4

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KX5

1kx5


Resolution: 1.31→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.749 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0562 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.055
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES REFINED INDIVIDUALLY ANISOTROPICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 1776 4.7 %RANDOM
Rwork0.1695 ---
obs0.1712 36283 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.57 Å2 / Biso mean: 20.418 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å2-0.01 Å2
2---0.96 Å20 Å2
3---0.33 Å2
Refinement stepCycle: final / Resolution: 1.31→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 9 43 1427
Biso mean--24.27 25.77 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191412
X-RAY DIFFRACTIONr_bond_other_d0.0020.021421
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9781909
X-RAY DIFFRACTIONr_angle_other_deg1.05733254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.55179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63422.20359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8315261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9371515
X-RAY DIFFRACTIONr_chiral_restr0.1010.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021570
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02323
X-RAY DIFFRACTIONr_rigid_bond_restr1.78832831
X-RAY DIFFRACTIONr_sphericity_free14.972522
X-RAY DIFFRACTIONr_sphericity_bonded5.96852833
LS refinement shellResolution: 1.315→1.349 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 143 -
Rwork0.304 2593 -
all-2736 -
obs--99.78 %

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