[English] 日本語
Yorodumi
- PDB-5zb3: Dimeric crystal structure of ORF57 from KSHV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zb3
TitleDimeric crystal structure of ORF57 from KSHV
ComponentsORF57
KeywordsTRANSCRIPTION / KSHV ORF57
Function / homologyHerpesvirus ICP27-like / Herpesvirus transcriptional regulator family / host cell cytoplasm / host cell nucleus / regulation of DNA-templated transcription / RNA binding / metal ion binding / ORF57 / mRNA export factor ICP27 homolog
Function and homology information
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ORF57
B: ORF57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6064
Polymers64,4752
Non-polymers1312
Water0
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more