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- PDB-9mt9: Candida albicans Hsp90 nucleotide binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9mt9
TitleCandida albicans Hsp90 nucleotide binding domain in complex with BTB10184
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
4-(4-hydroxyphenyl)sulfanylphenol / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsKowalewski, M.E. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM148376-01A1 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5692
Polymers26,3511
Non-polymers2181
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.252, 74.252, 107.189
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-487-

HOH

21A-527-

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-A8K / 4-(4-hydroxyphenyl)sulfanylphenol


Mass: 218.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H10O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.17 M ammonium acetate, 0.085 M sodium citrate:HCl pH 5.6, 25.5% w/v PEG4000, and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→37.13 Å / Num. obs: 29446 / % possible obs: 99.97 % / Redundancy: 19.8 % / Biso Wilson estimate: 26.61 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08041 / Net I/σ(I): 21.88
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 19.8 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.89 / Num. unique obs: 2053 / CC1/2: 0.864 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→37.13 Å / SU ML: 0.2199 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 2000 6.79 %
Rwork0.1896 27437 -
obs0.1916 29437 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.85 Å2
Refinement stepCycle: LAST / Resolution: 1.78→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 15 158 1856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01131790
X-RAY DIFFRACTIONf_angle_d1.11452436
X-RAY DIFFRACTIONf_chiral_restr0.0634283
X-RAY DIFFRACTIONf_plane_restr0.0097315
X-RAY DIFFRACTIONf_dihedral_angle_d15.5593682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.33461390.28321912X-RAY DIFFRACTION99.95
1.82-1.870.29351400.24321914X-RAY DIFFRACTION100
1.87-1.930.28361390.22121913X-RAY DIFFRACTION100
1.93-1.990.25941410.20871937X-RAY DIFFRACTION100
1.99-2.060.25211430.20621956X-RAY DIFFRACTION100
2.06-2.140.23951390.19711906X-RAY DIFFRACTION100
2.15-2.240.22221420.19311952X-RAY DIFFRACTION99.95
2.24-2.360.21961390.1871911X-RAY DIFFRACTION100
2.36-2.510.20681440.19991980X-RAY DIFFRACTION100
2.51-2.70.23751420.19421941X-RAY DIFFRACTION100
2.7-2.970.24841450.19591976X-RAY DIFFRACTION100
2.97-3.40.22721440.18451982X-RAY DIFFRACTION100
3.4-4.290.18831470.16742016X-RAY DIFFRACTION100
4.29-37.130.18851560.18142141X-RAY DIFFRACTION99.87

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