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

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Basic information

Entry
Database: PDB / ID: 9msv
TitleCandida albicans Hsp90 nucleotide binding domain in complex with BEP800
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-2KL / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8312
Polymers26,3511
Non-polymers4801
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.915, 73.915, 108.003
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-499-

HOH

21A-512-

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-2KL / 2-amino-4-[2,4-dichloro-5-(2-pyrrolidin-1-ylethoxy)phenyl]-N-ethylthieno[2,3-d]pyrimidine-6-carboxamide


Mass: 480.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23Cl2N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 56.06 %
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 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→47.05 Å / Num. obs: 18910 / % possible obs: 99.98 % / Redundancy: 19.5 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0718 / Net I/σ(I): 27.09
Reflection shellResolution: 2.07→2.1 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 5.74 / Num. unique obs: 1445 / CC1/2: 0.951 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→47.05 Å / SU ML: 0.2154 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2264 3514 10.08 %
Rwork0.1823 31348 -
obs0.1866 18907 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.01 Å2
Refinement stepCycle: LAST / Resolution: 2.07→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 31 130 1833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01161766
X-RAY DIFFRACTIONf_angle_d1.18642394
X-RAY DIFFRACTIONf_chiral_restr0.0609271
X-RAY DIFFRACTIONf_plane_restr0.0096308
X-RAY DIFFRACTIONf_dihedral_angle_d17.2585666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.10.29911400.21571261X-RAY DIFFRACTION100
2.1-2.130.26481370.21231261X-RAY DIFFRACTION100
2.13-2.160.29641400.21491244X-RAY DIFFRACTION100
2.16-2.190.2641440.20421238X-RAY DIFFRACTION100
2.19-2.230.28181440.20821266X-RAY DIFFRACTION99.86
2.23-2.270.24351410.20071249X-RAY DIFFRACTION100
2.27-2.310.25071400.19281258X-RAY DIFFRACTION100
2.31-2.350.22071430.21031244X-RAY DIFFRACTION100
2.35-2.40.27461360.21221250X-RAY DIFFRACTION100
2.4-2.450.29031400.20141252X-RAY DIFFRACTION100
2.45-2.510.19371430.19261269X-RAY DIFFRACTION100
2.51-2.570.251400.18291242X-RAY DIFFRACTION100
2.57-2.640.26841440.19711259X-RAY DIFFRACTION100
2.64-2.720.26751420.19061247X-RAY DIFFRACTION100
2.72-2.810.22071440.20211246X-RAY DIFFRACTION100
2.81-2.910.24461420.20021267X-RAY DIFFRACTION100
2.91-3.030.29591400.20551242X-RAY DIFFRACTION100
3.03-3.160.25041390.19721255X-RAY DIFFRACTION100
3.16-3.330.2441460.17591246X-RAY DIFFRACTION100
3.33-3.540.20881370.17921270X-RAY DIFFRACTION100
3.54-3.810.21351410.17391248X-RAY DIFFRACTION100
3.81-4.20.22221340.15261264X-RAY DIFFRACTION100
4.2-4.80.16191330.13341249X-RAY DIFFRACTION100
4.8-6.050.18351410.17121260X-RAY DIFFRACTION99.93
6.05-47.050.21461430.19621261X-RAY DIFFRACTION99.79

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