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- PDB-7k9s: Cryptococcus neoformans Hsp90 nucleotide binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7k9s
TitleCryptococcus neoformans Hsp90 nucleotide binding domain in complex with NVP-AUY922
ComponentsHsp90-like protein
KeywordsCHAPERONE / Cryptococcus / HSP90 / ATP-binding / Inhibitor
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Histidine kinase/HSP90-like ATPase / 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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases ...Histidine kinase/HSP90-like ATPase / 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-, 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-2GJ / Hsp90-like protein
Similarity search - Component
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI120958 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Fungal-Selective Resorcylate Aminopyrazole Hsp90 Inhibitors: Optimization of Whole-Cell Anticryptococcal Activity and Insights into the Structural Origins of Cryptococcal Selectivity.
Authors: Marcyk, P.T. / LeBlanc, E.V. / Kuntz, D.A. / Xue, A. / Ortiz, F. / Trilles, R. / Bengtson, S. / Kenney, T.M.G. / Huang, D.S. / Robbins, N. / Williams, N.S. / Krysan, D.J. / Prive, G.G. / ...Authors: Marcyk, P.T. / LeBlanc, E.V. / Kuntz, D.A. / Xue, A. / Ortiz, F. / Trilles, R. / Bengtson, S. / Kenney, T.M.G. / Huang, D.S. / Robbins, N. / Williams, N.S. / Krysan, D.J. / Prive, G.G. / Whitesell, L. / Cowen, L.E. / Brown, L.E.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: 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
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hsp90-like protein
B: Hsp90-like protein
C: Hsp90-like protein
D: Hsp90-like protein
E: Hsp90-like protein
F: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,70412
Polymers143,9116
Non-polymers2,7936
Water00
1
A: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4512
Polymers23,9851
Non-polymers4661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4512
Polymers23,9851
Non-polymers4661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4512
Polymers23,9851
Non-polymers4661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4512
Polymers23,9851
Non-polymers4661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4512
Polymers23,9851
Non-polymers4661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4512
Polymers23,9851
Non-polymers4661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.639, 78.450, 188.105
Angle α, β, γ (deg.)90.000, 95.743, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Hsp90-like protein


Mass: 23985.100 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: J9VVA4
#2: Chemical
ChemComp-2GJ / 5-[2,4-DIHYDROXY-5-(1-METHYLETHYL)PHENYL]-N-ETHYL-4-[4-(MORPHOLIN-4-YLMETHYL)PHENYL]ISOXAZOLE-3-CARBOXAMIDE


Mass: 465.541 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H31N3O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1M LiCl, Hepes pH 7, 20-25% PEG 6K, 10-20% DMSO / PH range: 6.5-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 3.21→18.21 Å / Num. obs: 24421 / % possible obs: 98.65 % / Redundancy: 5.2 % / Biso Wilson estimate: 85.64 Å2 / CC1/2: 0.996 / Net I/σ(I): 6.04
Reflection shellResolution: 3.21→3.24 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.323 / Num. unique obs: 2323 / CC1/2: 0.65 / % possible all: 96.43

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CJI

6cji


Resolution: 3.21→18.21 Å / SU ML: 0.4263 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.0103
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2512 2301 4.93 %
Rwork0.2124 44399 -
obs0.2143 46700 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.3 Å2
Refinement stepCycle: LAST / Resolution: 3.21→18.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9924 0 204 0 10128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004710308
X-RAY DIFFRACTIONf_angle_d0.7413914
X-RAY DIFFRACTIONf_chiral_restr0.05911570
X-RAY DIFFRACTIONf_plane_restr0.00291759
X-RAY DIFFRACTIONf_dihedral_angle_d18.22213830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.280.34241120.31622458X-RAY DIFFRACTION86.47
3.28-3.350.33981360.32812585X-RAY DIFFRACTION90.25
3.35-3.440.34191390.3232600X-RAY DIFFRACTION90.4
3.44-3.530.32161480.27292731X-RAY DIFFRACTION99.31
3.53-3.630.32091540.26182871X-RAY DIFFRACTION100
3.63-3.750.35671400.24432873X-RAY DIFFRACTION99.8
3.75-3.880.26951560.22772791X-RAY DIFFRACTION99.93
3.88-4.030.29421440.2172845X-RAY DIFFRACTION99.83
4.04-4.220.21641450.20662849X-RAY DIFFRACTION100
4.22-4.440.24971390.19752827X-RAY DIFFRACTION99.66
4.44-4.710.19311460.18532883X-RAY DIFFRACTION99.84
4.71-5.070.23961470.20752768X-RAY DIFFRACTION99.25
5.07-5.560.25031440.20792846X-RAY DIFFRACTION99.97
5.56-6.340.31491540.22942847X-RAY DIFFRACTION99.97
6.34-7.870.20611570.19362840X-RAY DIFFRACTION99.93
7.88-18.210.18511400.14762785X-RAY DIFFRACTION98.09

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