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- PDB-9msu: Candida albicans Hsp90 nucleotide binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9msu
TitleCandida albicans Hsp90 nucleotide binding domain in complex with BX2819
ComponentsHeat shock protein 90 homolog
KeywordsCHAPERONE/INHIBITOR / Inhibitor complex / CHAPERONE / CHAPERONE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of filamentous growth of a population of unicellular organisms / filamentous growth of a population of unicellular organisms / hyphal cell wall / fungal-type cell wall / filamentous growth / nuclear receptor-mediated steroid hormone signaling pathway / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / extracellular vesicle ...negative regulation of filamentous growth of a population of unicellular organisms / filamentous growth of a population of unicellular organisms / hyphal cell wall / fungal-type cell wall / filamentous growth / nuclear receptor-mediated steroid hormone signaling pathway / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / extracellular vesicle / cellular response to heat / regulation of apoptotic process / protein stabilization / perinuclear region of cytoplasm / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-819 / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsKowalewski, M.E. / Redinbo, M.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM148376-01A1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM152079-01 United States
CitationJournal: Biochemistry / Year: 2025
Title: Structural Insights into Selectively Targeting Candida albicans Hsp90.
Authors: Kowalewski, M.E. / Zagler, S. / Redinbo, M.R.
History
DepositionJan 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8413
Polymers26,3511
Non-polymers4912
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.225, 74.225, 107.712
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-583-

HOH

21A-606-

HOH

31A-609-

HOH

41A-689-

HOH

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Components

#1: Protein Heat shock protein 90 homolog


Mass: 26350.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast)
Gene: HSP90, CAALFM_C702030WA, CaJ7.0234, CaO19.13868, CaO19.6515
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P46598
#2: Chemical ChemComp-819 / ethyl (4-{3-[2,4-dihydroxy-5-(1-methylethyl)phenyl]-5-sulfanyl-4H-1,2,4-triazol-4-yl}benzyl)carbamate


Mass: 428.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES:NaOH, pH 6.5 10% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→37.59 Å / Num. obs: 43441 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 21.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04946 / Net I/σ(I): 18.2
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 3007 / CC1/2: 0.866 / % possible all: 98.72

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHASERphasing
AutoProcessdata processing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→37.59 Å / SU ML: 0.1706 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.3443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1977 2000 4.61 %
Rwork0.178 41353 -
obs0.1794 43351 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.21 Å2
Refinement stepCycle: LAST / Resolution: 1.56→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 34 291 2014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01711805
X-RAY DIFFRACTIONf_angle_d1.44332451
X-RAY DIFFRACTIONf_chiral_restr0.0804279
X-RAY DIFFRACTIONf_plane_restr0.0119318
X-RAY DIFFRACTIONf_dihedral_angle_d15.0181677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.30531390.25872868X-RAY DIFFRACTION98.75
1.6-1.640.24051410.23352924X-RAY DIFFRACTION100
1.64-1.690.25291410.21462930X-RAY DIFFRACTION100
1.69-1.750.21381420.19592917X-RAY DIFFRACTION99.97
1.75-1.810.23841410.19422925X-RAY DIFFRACTION100
1.81-1.880.23251410.20092907X-RAY DIFFRACTION99.93
1.88-1.970.23591410.20062919X-RAY DIFFRACTION99.29
1.97-2.070.23861430.18322954X-RAY DIFFRACTION100
2.07-2.20.18131420.17612940X-RAY DIFFRACTION100
2.2-2.370.18691440.17262967X-RAY DIFFRACTION99.97
2.37-2.610.18421440.16972970X-RAY DIFFRACTION99.87
2.61-2.980.16711440.16722992X-RAY DIFFRACTION99.4
2.98-3.760.20071480.16063041X-RAY DIFFRACTION99.97
3.76-37.590.18481490.1793099X-RAY DIFFRACTION96.29

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