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

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Basic information

Entry
Database: PDB / ID: 9mtb
TitleCandida albicans Hsp90 nucleotide binding domain in complex with AMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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)26,8572
Polymers26,3511
Non-polymers5061
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.162, 74.162, 107.610
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

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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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
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 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→31.7 Å / Num. obs: 10547 / % possible obs: 99.88 % / Redundancy: 14.3 % / Biso Wilson estimate: 47.67 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1054 / Net I/σ(I): 15.68
Reflection shellResolution: 2.53→2.64 Å / Redundancy: 15 % / Rmerge(I) obs: 0.5638 / Mean I/σ(I) obs: 4.63 / Num. unique obs: 1286 / CC1/2: 0.934 / % possible all: 99.64

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→31.7 Å / SU ML: 0.3088 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2693 1055 10 %
Rwork0.2058 9492 -
obs0.2121 10547 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.62 Å2
Refinement stepCycle: LAST / Resolution: 2.53→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 31 16 1708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421719
X-RAY DIFFRACTIONf_angle_d1.49442331
X-RAY DIFFRACTIONf_chiral_restr0.0666269
X-RAY DIFFRACTIONf_plane_restr0.0115296
X-RAY DIFFRACTIONf_dihedral_angle_d17.741651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.650.30711290.25131158X-RAY DIFFRACTION99.54
2.65-2.780.27961280.23051156X-RAY DIFFRACTION99.61
2.79-2.960.24821290.21671158X-RAY DIFFRACTION99.77
2.96-3.190.31711290.24431166X-RAY DIFFRACTION99.69
3.19-3.510.27811290.21791162X-RAY DIFFRACTION99.85
3.51-4.010.29731320.19991182X-RAY DIFFRACTION99.92
4.01-5.050.20161350.17181217X-RAY DIFFRACTION100
5.06-31.70.29531440.20591293X-RAY DIFFRACTION100

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