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- PDB-9d9f: Candida albicans Hsp90 nucleotide binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9d9f
TitleCandida albicans Hsp90 nucleotide binding domain in complex with BRI2311
ComponentsHeat shock protein 90 homolog
KeywordsCHAPERONE / HSP90 nucleotide binding domain 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
: / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To be published
Title: Final Title 'To Be Determined'
Authors: Kuntz, D.A. / Prive, G.G.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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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)25,6603
Polymers24,9101
Non-polymers7502
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.874, 73.874, 108.817
Angle α, β, γ (deg.)90, 90, 90
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

21A-576-

HOH

31A-615-

HOH

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Components

#1: Protein Heat shock protein 90 homolog


Mass: 24910.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast)
Gene: HSP90, CAALFM_C702030WA, CaJ7.0234, CaO19.13868, CaO19.6515
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P46598
#2: Chemical ChemComp-A1A26 / (1P)-3-amino-6-[({1-[(2S)-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]piperidin-4-yl}amino)methyl]-1-(4-phenyl-3,4-dihydro-2H-1,4-benzoxazin-6-yl)thieno[2,3-b]pyrazin-2(1H)-one


Mass: 725.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H37F2N9O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 18% PEG8000, 0.1M Cacodylates pH 6.5, 0.2 M MgAcetate, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54189 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: May 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54189 Å / Relative weight: 1
ReflectionResolution: 1.75→30.56 Å / Num. obs: 31120 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Net I/σ(I): 31 / Num. measured all: 395944
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 99.4 % / Redundancy: 4 % / Rmerge(I) obs: 1.145 / Num. measured all: 6540 / Num. unique obs: 1651 / CC1/2: 0.546 / Rpim(I) all: 0.635 / Rrim(I) all: 1.317 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→30.56 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.373 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1985 1480 5 %
Rwork0.1752 28121 -
all0.176 --
obs-29601 99.936 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.622 Å2
Baniso -1Baniso -2Baniso -3
1--0.642 Å20 Å20 Å2
2---0.642 Å20 Å2
3---1.284 Å2
Refinement stepCycle: LAST / Resolution: 1.78→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 53 283 2031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121942
X-RAY DIFFRACTIONr_bond_other_d0.0080.0161833
X-RAY DIFFRACTIONr_angle_refined_deg2.2471.8622641
X-RAY DIFFRACTIONr_angle_other_deg1.2941.7814229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5975244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.48158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8810347
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.1321088
X-RAY DIFFRACTIONr_chiral_restr0.1150.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022288
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02428
X-RAY DIFFRACTIONr_nbd_refined0.170.2343
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1190.21602
X-RAY DIFFRACTIONr_nbtor_refined0.1420.2927
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0610.2965
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2225
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0470.221
X-RAY DIFFRACTIONr_nbd_other0.0690.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0510.238
X-RAY DIFFRACTIONr_mcbond_it2.9412.355955
X-RAY DIFFRACTIONr_mcbond_other2.9412.355955
X-RAY DIFFRACTIONr_mcangle_it4.6574.2111206
X-RAY DIFFRACTIONr_mcangle_other4.6554.2151207
X-RAY DIFFRACTIONr_scbond_it3.5152.529987
X-RAY DIFFRACTIONr_scbond_other3.5072.53987
X-RAY DIFFRACTIONr_scangle_it5.4274.561435
X-RAY DIFFRACTIONr_scangle_other5.4254.561436
X-RAY DIFFRACTIONr_lrange_it7.98124.7252274
X-RAY DIFFRACTIONr_lrange_other7.64722.7322172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.78-1.8260.3341080.27620360.27921490.9270.94199.76730.248
1.826-1.8760.2211010.24819820.24620830.9690.9571000.208
1.876-1.930.2521020.2219350.22220370.960.9661000.18
1.93-1.9890.2171000.21618630.21619630.9690.9671000.178
1.989-2.0540.234950.19818380.219330.9560.9731000.163
2.054-2.1260.196950.1817670.1818620.9740.9791000.15
2.126-2.2060.178860.16916840.16917700.980.9821000.135
2.206-2.2950.23910.17116550.17417460.9690.9811000.139
2.295-2.3970.174810.16215910.16316720.9790.9831000.131
2.397-2.5130.195800.1715080.17215880.9740.9811000.138
2.513-2.6480.191760.15814500.15915260.9760.9841000.128
2.648-2.8070.183720.17213790.17314510.9770.9821000.142
2.807-2.9990.166690.15312970.15413660.9810.9851000.128
2.999-3.2370.187650.14912160.15112820.9770.98699.9220.128
3.237-3.5420.187570.15511280.15711860.9790.98599.91570.137
3.542-3.9540.193550.15510230.15710780.9790.9861000.14
3.954-4.5520.155480.1419250.1429740.9880.98899.89730.128
4.552-5.5450.166420.167900.168320.9870.9871000.143
5.545-7.7160.236330.2336420.2336750.9730.9661000.209
7.716-30.560.263230.2154120.2184350.9330.9641000.201

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