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- PDB-6lmh: Structure of an ASFV-derived histone-like protein pA104R -

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Basic information

Entry
Database: PDB / ID: 6lmh
TitleStructure of an ASFV-derived histone-like protein pA104R
ComponentspA104R
KeywordsDNA BINDING PROTEIN / apo state
Function / homology
Function and homology information


virion component / structural constituent of chromatin / DNA replication / DNA binding
Similarity search - Function
HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Viral histone-like protein / Viral histone-like protein
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.805 Å
AuthorsWang, H. / Qi, J. / Chai, Y. / Gao, F.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31941003 China
Chinese Academy of SciencesKJZD-SW-L06-01 China
National Natural Science Foundation of China (NSFC)31700149 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: The structural basis of African swine fever virus pA104R binding to DNA and its inhibition by stilbene derivatives.
Authors: Liu, R. / Sun, Y. / Chai, Y. / Li, S. / Li, S. / Wang, L. / Su, J. / Yu, S. / Yan, J. / Gao, F. / Zhang, G. / Qiu, H.J. / Gao, G.F. / Qi, J. / Wang, H.
History
DepositionDec 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: pA104R
B: pA104R


Theoretical massNumber of molelcules
Total (without water)24,9192
Polymers24,9192
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-44 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.618, 58.618, 150.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein pA104R / pA104R / A104R CDS protein / BA71V-A104R / Histone-like protein / PA104R


Mass: 12459.636 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus
Gene: A104R, A104R CDS, BA71V-A104R, AFSV47Ss_0056, ASFV-Georgia_4-058
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1E0L7, UniProt: P68742*PLUS

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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: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M citric acid, pH 4.5, 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 7855 / % possible obs: 99.6 % / Redundancy: 18.8 % / CC1/2: 0.983 / Net I/σ(I): 48.133
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 754 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 2.805→42.092 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.17
RfactorNum. reflection% reflection
Rfree0.2991 393 5.2 %
Rwork0.2533 --
obs0.2558 7551 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.805→42.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 0 0 1554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091582
X-RAY DIFFRACTIONf_angle_d0.9052140
X-RAY DIFFRACTIONf_dihedral_angle_d18.975624
X-RAY DIFFRACTIONf_chiral_restr0.06256
X-RAY DIFFRACTIONf_plane_restr0.006272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.805-3.21060.35971060.29972156X-RAY DIFFRACTION89
3.2106-4.04460.32731560.26772420X-RAY DIFFRACTION100
4.0446-42.090.25841310.22762582X-RAY DIFFRACTION100

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