[English] 日本語
Yorodumi
- PDB-5yzl: Crystal structure of human Archease D178A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yzl
TitleCrystal structure of human Archease D178A
ComponentsProtein archease
KeywordsCHAPERONE / a cofactor of RTCB
Function / homologyArchease / Archease domain / Archease domain superfamily / Archease protein family (MTH1598/TM1083) / tRNA processing / metal ion binding / Protein archease
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsDuan, S.Y. / Li, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Structural and mechanistic insights into human Archease mutant D178A
Authors: Duan, S.Y. / Li, J.X.
History
DepositionDec 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein archease
B: Protein archease


Theoretical massNumber of molelcules
Total (without water)43,5872
Polymers43,5872
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-17 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.686, 59.620, 133.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein archease / cDNA FLJ75987 / highly similar to Homo sapiens zinc finger and BTB domain containing 8 opposite ...cDNA FLJ75987 / highly similar to Homo sapiens zinc finger and BTB domain containing 8 opposite strand (ZBTB8OS) / mRNA


Mass: 21793.312 Da / Num. of mol.: 2 / Mutation: D178A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB8OS / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: A8K0B5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, 100mM HEPES/Sodium hydroxide pH 7.5, 200mM Magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.0688 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0688 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 5767 / % possible obs: 98.6 % / Redundancy: 10.5 % / Net I/σ(I): 2
Reflection shellResolution: 3.4→3.46 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YZ1

5yz1


Resolution: 3.4→45.73 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection
Rfree0.2512 314
Rwork0.1881 -
obs-5453
Refinement stepCycle: LAST / Resolution: 3.4→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 0 9 2617

+
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