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- PDB-8yjg: Crystal structure of the nucleotide-binding domain of Candida gla... -

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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: Biodesign / Year: 2024
Title: Crystal structure of the N-terminal 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
Revision 1.1Sep 24, 2025Group: Database references / Category: citation
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.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 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

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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

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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

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