[English] 日本語
Yorodumi
- PDB-8yjg: Crystal structure of the nucleotide-binding domain of Candida gla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yjg
TitleCrystal structure of the nucleotide-binding domain of Candida glabrata Hsp90
ComponentsATP-dependent molecular chaperone HSC82
KeywordsCHAPERONE / Hsp90 / ATPase
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ATP-dependent molecular chaperone HSC82
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTan, L. / Li, X. / Zhang, G. / Chen, L. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00241410 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of the nucleotide-binding domain of Candida glabrata Hsp90
Authors: Tan, L. / Li, X. / Zhang, G. / Chen, L. / Im, Y.J.
History
DepositionMar 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent molecular chaperone HSC82


Theoretical massNumber of molelcules
Total (without water)24,3871
Polymers24,3871
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.942, 73.942, 108.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

21A-446-

HOH

31A-469-

HOH

-
Components

#1: Protein ATP-dependent molecular chaperone HSC82


Mass: 24386.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The nucleotide-binding domain of C.g. Hsp90. The N-terminal GSAMGS is a linker sequence for the N-terminal cleavable His-tag fusion originating from the plasmid.
Source: (gene. exp.) Candida glabrata (fungus) / Gene: hsp90 / Plasmid: pHIS2-thr
Details (production host): The N-terminal His-tag fusion cleavable by thrombin protease
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0W0DX49
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 70% (v/v) 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 24325 / % possible obs: 99.4 % / Redundancy: 7.6 % / Biso Wilson estimate: 29.36 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 48.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 1193 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30.57 Å / SU ML: 0.1951 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.6914
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2251 1997 8.23 %
Rwork0.2027 22258 -
obs0.2046 24255 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.32 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 0 176 1860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671708
X-RAY DIFFRACTIONf_angle_d0.88252301
X-RAY DIFFRACTIONf_chiral_restr0.0542266
X-RAY DIFFRACTIONf_plane_restr0.0062295
X-RAY DIFFRACTIONf_dihedral_angle_d14.3388648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.27191400.22991557X-RAY DIFFRACTION99.41
1.95-20.28511410.22211562X-RAY DIFFRACTION100
2-2.060.27351400.20061568X-RAY DIFFRACTION99.88
2.06-2.130.26091410.19761561X-RAY DIFFRACTION99.82
2.13-2.20.23621420.20721577X-RAY DIFFRACTION99.88
2.2-2.290.2521390.20791564X-RAY DIFFRACTION99.77
2.29-2.390.24811420.20691594X-RAY DIFFRACTION99.77
2.39-2.520.25811420.20781580X-RAY DIFFRACTION99.94
2.52-2.680.22441430.21121593X-RAY DIFFRACTION100
2.68-2.880.22491420.21451587X-RAY DIFFRACTION99.71
2.88-3.170.23171450.20541616X-RAY DIFFRACTION99.94
3.17-3.630.21971460.1921625X-RAY DIFFRACTION99.89
3.63-4.570.18651480.17411636X-RAY DIFFRACTION99.11
4.58-30.570.21861460.22521638X-RAY DIFFRACTION93.01

+
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