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- PDB-6lmj: ASFV pA104R in complex with double-strand DNA -

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Basic information

Entry
Database: PDB / ID: 6lmj
TitleASFV pA104R in complex with double-strand DNA
Components
  • A104R
  • DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*A)-3')
KeywordsDNA BINDING PROTEIN/DNA / Complex / dsDNA / ASFV / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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
DNA / DNA (> 10) / Viral histone-like protein / Viral histone-like protein
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, H. / Qi, J. / Chai, Y. / Gao, F. / Liu, R.
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 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: A104R
B: A104R
C: DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)36,5214
Polymers36,5214
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-70 kcal/mol
Surface area18710 Å2
Unit cell
Length a, b, c (Å)82.358, 89.095, 53.227
Angle α, β, γ (deg.)90.00, 100.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein A104R / 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
#2: DNA chain DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*A)-3') / 20 bp double-strand DNA


Mass: 5800.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M imidazole malate, pH 7.0, 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9113 / % possible obs: 96.2 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 20.619
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 931 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LMH

6lmh


Resolution: 2.8→27.886 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.54
RfactorNum. reflection% reflection
Rfree0.2848 395 4.45 %
Rwork0.2559 --
obs0.2572 8870 93.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→27.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 768 0 16 2329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042429
X-RAY DIFFRACTIONf_angle_d0.7033446
X-RAY DIFFRACTIONf_dihedral_angle_d27.29991
X-RAY DIFFRACTIONf_chiral_restr0.043405
X-RAY DIFFRACTIONf_plane_restr0.004308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-3.19070.36681480.32372786X-RAY DIFFRACTION93
3.1907-4.0180.37121100.29452631X-RAY DIFFRACTION87
4.018-27.880.20081370.20913058X-RAY DIFFRACTION100
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)
10.3937-0.3088-0.21391.1242-1.12111.09850.02610.0515-0.04960.0208-0.1693-0.032-0.15810.1739-0.03030.1374-0.0662-0.04240.2183-0.02340.264221.6689-19.41877.4131
20.753-0.3113-0.87641.45260.15990.95170.0649-0.0056-0.1457-0.0089-0.22170.0363-0.0555-0.0181-0.01240.0645-0.0251-0.01830.13980.01040.201616.841-29.43376.4535
30.14610.0147-0.01780.05370.00520.08660.09410.27520.06630.2648-0.55210.11840.4192-1.0739-0.3540.63110.05120.13150.6037-0.22830.392715.225-2.37570.8801
40.45560.35650.05370.3156-0.07630.0094-0.09930.1782-0.0304-0.2193-0.1464-0.1533-0.1056-0.8288-0.21490.5299-0.0177-0.0950.5744-0.19730.264216.0064-2.0115-2.8393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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