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- PDB-9mt3: Candida albicans Hsp90 nucleotide binding domain in complex with XL888 -

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Basic information

Entry
Database: PDB / ID: 9mt3
TitleCandida albicans Hsp90 nucleotide binding domain in complex with XL888
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 / cytoplasm / cytosol
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 superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-99B / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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)26,8542
Polymers26,3511
Non-polymers5041
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.337, 108.946, 50.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

21A-470-

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-99B / 5-[(2R)-butan-2-ylamino]-N-{(3-endo)-8-[5-(cyclopropylcarbonyl)pyridin-2-yl]-8-azabicyclo[3.2.1]oct-3-yl}-2-methylbenzene-1,4-dicarboxamide


Mass: 503.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H37N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05M CaCl2, 0.1M Bis-Tris (pH6.5) and 30% v/v PEG 550 MME

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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: Aug 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→32.59 Å / Num. obs: 15170 / % possible obs: 99.96 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1113 / Net I/σ(I): 9.8
Reflection shellResolution: 2.02→2.09 Å / Rmerge(I) obs: 0.6042 / Mean I/σ(I) obs: 2.57 / Num. unique obs: 1347 / CC1/2: 0.889 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHENIXphasing
AutoProcessdata processing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→32.59 Å / SU ML: 0.2466 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2443 1517 10 %
Rwork0.1876 13648 -
obs0.1931 15165 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.77 Å2
Refinement stepCycle: LAST / Resolution: 2.02→32.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 37 118 1809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01161734
X-RAY DIFFRACTIONf_angle_d1.1182344
X-RAY DIFFRACTIONf_chiral_restr0.0549266
X-RAY DIFFRACTIONf_plane_restr0.0093301
X-RAY DIFFRACTIONf_dihedral_angle_d17.0203671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.090.30971350.24521212X-RAY DIFFRACTION100
2.09-2.160.31851340.22951211X-RAY DIFFRACTION99.85
2.16-2.250.31361370.21961225X-RAY DIFFRACTION100
2.25-2.350.27951380.21421239X-RAY DIFFRACTION100
2.35-2.470.27541340.20031210X-RAY DIFFRACTION99.85
2.47-2.630.26981370.19751237X-RAY DIFFRACTION99.93
2.63-2.830.28541380.20721245X-RAY DIFFRACTION100
2.83-3.110.26341370.19181229X-RAY DIFFRACTION100
3.11-3.560.22681390.18611245X-RAY DIFFRACTION100
3.57-4.490.19081400.15131267X-RAY DIFFRACTION100
4.49-32.590.21171480.17411328X-RAY DIFFRACTION99.93

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