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- PDB-5zb3: Dimeric crystal structure of ORF57 from KSHV -

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Basic information

Entry
Database: PDB / ID: 5zb3
TitleDimeric crystal structure of ORF57 from KSHV
ComponentsORF57
KeywordsTRANSCRIPTION / KSHV ORF57
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of viral life cycle / protein sequestering activity / host cell cytoplasm / regulation of DNA-templated transcription / host cell nucleus / RNA binding / zinc ion binding
Similarity search - Function
Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family
Similarity search - Domain/homology
ORF57 / Post-transcriptional regulator MTA
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.506 Å
AuthorsGao, Z.Q. / Yuan, F. / Dong, Y.H. / Lan, K.
Funding support China, 2items
OrganizationGrant numberCountry
XDB08030103 China
2017YFA0504900 China
CitationJournal: PLoS Pathog. / Year: 2018
Title: The crystal structure of KSHV ORF57 reveals dimeric active sites important for protein stability and function.
Authors: Yuan, F. / Gao, Z.Q. / Majerciak, V. / Bai, L. / Hu, M.L. / Lin, X.X. / Zheng, Z.M. / Dong, Y.H. / Lan, K.
History
DepositionFeb 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

Downloads & links

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Assembly

Deposited unit
A: ORF57
B: ORF57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6064
Polymers64,4752
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-40 kcal/mol
Surface area26630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.529, 167.529, 227.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein ORF57


Mass: 32237.393 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF57 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0N9SHG8, UniProt: Q2HR75*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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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: 7.15 Å3/Da / Density % sol: 82.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.01M Magnesium chloride, 0.05M Hepes sodium pH 7.0, 4M Lithium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 24306 / % possible obs: 99.8 % / Redundancy: 10.3 % / CC1/2: 0.955 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.046 / Rrim(I) all: 0.149 / Net I/σ(I): 26.4
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1185 / CC1/2: 0.948 / Rpim(I) all: 0.259 / Rrim(I) all: 0.846 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.506→33.149 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.42
RfactorNum. reflection% reflection
Rfree0.306 1136 4.76 %
Rwork0.2571 --
obs0.2593 23848 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.506→33.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 0 2 0 4412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044504
X-RAY DIFFRACTIONf_angle_d0.8546086
X-RAY DIFFRACTIONf_dihedral_angle_d12.3792696
X-RAY DIFFRACTIONf_chiral_restr0.043682
X-RAY DIFFRACTIONf_plane_restr0.006784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5055-3.66490.41451440.33972772X-RAY DIFFRACTION99
3.6649-3.85780.39481480.31652755X-RAY DIFFRACTION98
3.8578-4.09910.30911400.29042735X-RAY DIFFRACTION97
4.0991-4.4150.32081140.24782788X-RAY DIFFRACTION97
4.415-4.8580.28571500.23472762X-RAY DIFFRACTION97
4.858-5.55810.29081410.2582881X-RAY DIFFRACTION99
5.5581-6.99180.37961530.29642919X-RAY DIFFRACTION100
6.9918-33.15050.23781460.21733100X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 62.7194 Å / Origin y: -58.2424 Å / Origin z: -14.0732 Å
111213212223313233
T0.671 Å20.0193 Å2-0.036 Å2-1.2213 Å2-0.0444 Å2--0.8376 Å2
L1.8044 °20.7195 °20.0467 °2-1.3262 °20.1993 °2--2.0217 °2
S-0.0495 Å °-0.404 Å °0.0355 Å °-0.0054 Å °-0.0822 Å °0.1455 Å °-0.1712 Å °-0.2264 Å °0.1226 Å °
Refinement TLS groupSelection details: all

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