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- PDB-7k9r: Cryptococcus neoformans Hsp90 nucleotide binding domain -

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Basic information

Entry
Database: PDB / ID: 7k9r
TitleCryptococcus neoformans Hsp90 nucleotide binding domain
ComponentsHsp90-like protein
KeywordsCHAPERONE / Crytococcus neoformans / HSP90 ATP-binding
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / plasma membrane / 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-, 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 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Biological speciesCryptococcus neoformans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKuntz, D.A. / Kenney, T. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0265
Polymers71,9553
Non-polymers712
Water7,368409
1
A: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0212
Polymers23,9851
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0212
Polymers23,9851
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hsp90-like protein


Theoretical massNumber of molelcules
Total (without water)23,9851
Polymers23,9851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.230, 80.260, 149.890
Angle α, β, γ (deg.)90.000, 92.319, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-301-

CL

21B-421-

HOH

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Components

#1: Protein Hsp90-like protein


Mass: 23985.100 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (fungus)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: J9VVA4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1M LiCL, Hepes pH7, 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: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→29.95 Å / Num. obs: 48718 / % possible obs: 85.22 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03001 / Net I/σ(I): 16.76
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.14 / Num. unique obs: 4717 / CC1/2: 0.71 / % possible all: 83.4

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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: 1.95→29.95 Å / SU ML: 0.207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2004 3414 3.64 %
Rwork0.168 90411 -
obs0.1692 93825 83.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.99 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 2 409 5397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01025139
X-RAY DIFFRACTIONf_angle_d1.17866938
X-RAY DIFFRACTIONf_chiral_restr0.0798797
X-RAY DIFFRACTIONf_plane_restr0.0081887
X-RAY DIFFRACTIONf_dihedral_angle_d14.84131928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.27861160.26813070X-RAY DIFFRACTION68.46
1.98-2.010.3051580.24914111X-RAY DIFFRACTION90.44
2.01-2.040.29591360.25353820X-RAY DIFFRACTION87.04
2.04-2.05X-RAY DIFFRACTION5
2.09-2.110.2698630.23621360X-RAY DIFFRACTION73.73
2.11-2.150.27371530.22224465X-RAY DIFFRACTION98.03
2.15-2.190.20881620.20134414X-RAY DIFFRACTION97.97
2.19-2.230.29851600.20114091X-RAY DIFFRACTION90.27
2.23-2.280.2853870.2042504X-RAY DIFFRACTION54.98
2.28-2.330.2311740.18354366X-RAY DIFFRACTION99.19
2.33-2.390.21791620.18534493X-RAY DIFFRACTION99.42
2.39-2.460.24621830.18684505X-RAY DIFFRACTION99.36
2.46-2.530.22281550.17974398X-RAY DIFFRACTION98.7
2.53-2.610.21551670.18344505X-RAY DIFFRACTION97.66
2.61-2.70.2752190.2178370X-RAY DIFFRACTION8.48
2.7-2.810.19541740.18714418X-RAY DIFFRACTION98.31
2.81-2.940.21371720.18084438X-RAY DIFFRACTION98.5
2.94-3.10.17941620.1694491X-RAY DIFFRACTION98.73
3.1-3.290.18311690.15724460X-RAY DIFFRACTION98.78
3.29-3.540.20061620.15024384X-RAY DIFFRACTION98.06
3.54-3.90.17441710.14474351X-RAY DIFFRACTION96.38
3.9-4.460.14571650.12944458X-RAY DIFFRACTION98.28
4.46-5.610.17511630.13724484X-RAY DIFFRACTION99.51
5.62-29.950.18971810.16684436X-RAY DIFFRACTION98.67
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.632026806281.16989167363-0.442332323833.44950197027-0.04458675278792.924505908640.00983440741550.1634606417880.118946404346-0.09449422038480.071203330718-0.00624890804659-0.08584003447230.13732170742-0.04903122077930.155728642469-0.01472357092510.01761224100890.1650136467660.01265172906820.13940267961612.14385630023.5995260259134.1569618869
22.29681402402-0.2258950004310.5059436288982.80214179239-0.8161131495934.629636956090.042743366995-0.1705065525370.1122385683250.4478997470790.07397414297720.225591627173-0.172822500259-0.0913146826565-0.09511210363310.200282185928-0.01667959729610.06377670735090.119870285503-0.003885434824190.201644151542-0.1745284364961.3747254436753.6697245751
32.652823185450.00111774253488-0.8516895305282.779751743630.5615899261283.40444801358-0.009842562072920.08789181642310.00257080289125-0.04717328780440.0880756369271-0.1181625598140.09507955230940.185487223138-0.09031985904480.132063836755-0.02144520157350.003790819535040.1132658221810.01768669884820.1703883296897.663474227690.72427947803541.1392339293
42.980407701380.365626603928-1.266290189241.88173277946-0.3297176782032.263384072620.08875082265880.1543510641040.1830630790070.05186375990740.04837396666370.222421255895-0.188129290159-0.187365762446-0.1122643308930.1791040404060.03421983691560.01007164678510.09668515170760.01058652665310.191605664831-1.232021311156.7648067233343.7303558063
53.44346292211-0.0328305771127-1.106595697214.822748414330.7792618995765.00322230551-0.08132492677170.199838722662-0.1439421073520.093938266255-0.05569317244310.2359637212970.199154936441-0.09373255539160.138393901870.264733405812-0.009056876648690.06023118569660.2267927125350.001801256027920.125862675755-1.02841847901-21.185414709567.5133510685
62.295942558531.59843654425-0.2585165505495.38162142118-0.8281444643052.599401004770.01382802508130.0443923941297-0.118448288067-0.0941709032383-0.300122089329-0.5431652813330.08553337930310.2877150112170.2043873063030.1249716692210.06572821356470.00640483330440.2468031064950.02188282443230.18007285924914.8006833563-19.151047429153.6917586191
75.30050032465-1.1044780392-0.4685457184273.48169517942-0.7403721627362.661945726870.140701499940.126308454297-0.02678831169880.13301440602-0.03848196427590.381150909023-0.104449617276-0.286021975001-0.09046139879930.1930997244130.006819126502150.02067633177480.2049858417770.01001633653350.166254292436-0.262818597636-12.837375646660.4449363601
82.1467812716-0.46506298681-0.8995318849463.110344165940.2949249306862.50201369526-0.05253415304240.0017305272338-0.178224220032-0.0184220417678-0.139098316602-0.08397254220720.1412242977710.07419151450090.1717666462880.1424298856330.0347367146278-0.02279847587070.1783763058680.03587772265830.16379739359710.5098382916-25.165027645659.1081640818
92.479728824830.942506243365-1.107195384792.25417951866-0.6165679027933.85823317167-0.06675344320890.000106024583954-0.319803886549-0.176728672317-0.126247799492-0.352699752950.1744769730980.4635574641510.0755445680740.1352574459380.0145126140622-0.009435034561110.254873914657-0.01270219906970.2064270657960.82801895226-30.344005016520.0675136304
102.89337156612-0.135651437567-0.9267559572324.4812328065-0.2580960190562.430648425690.04757940551710.0322421387845-0.401137084865-0.246066401338-0.160524608331-0.02262992756990.1622774170680.165618011510.111944194040.217060394559-0.01285452846690.007007374804370.264805742364-0.03890624162410.238236302504-2.67819724987-31.575319973112.6461422565
115.762936235152.126648574090.1722841257972.812920918361.193040954726.552825426210.240750339354-0.334400370732-0.1690988815150.114292368297-0.2678540504810.007522310969120.1648684358880.2687535044580.03674051445810.208338492587-0.0157336779984-0.04274852474530.274166626097-0.004876410101070.216986375683-0.566764832916-23.50058823733.0203087517
122.376967691870.884319473778-1.395537179192.40165766383-1.520148887294.89452377593-0.02939802376330.0875996283824-0.163360941184-0.209686233548-0.0726748348075-0.06344037752240.1372090416580.03989915886750.07392043764850.148811786011-0.00415180238309-0.006507601688060.198309268544-0.0570060699040.149389862968-4.58656533214-28.126375874313.4678600606
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 26 )AA-1 - 261 - 27
22chain 'A' and (resid 27 through 69 )AA27 - 6928 - 70
33chain 'A' and (resid 70 through 139 )AA70 - 13971 - 144
44chain 'A' and (resid 140 through 211 )AA140 - 211145 - 216
55chain 'B' and (resid -1 through 26 )BD-1 - 261 - 28
66chain 'B' and (resid 27 through 79 )BD27 - 7929 - 82
77chain 'B' and (resid 80 through 122 )BD80 - 12283 - 126
88chain 'B' and (resid 123 through 211 )BD123 - 211127 - 216
99chain 'C' and (resid 2 through 62 )CG2 - 621 - 61
1010chain 'C' and (resid 63 through 93 )CG63 - 9362 - 93
1111chain 'C' and (resid 94 through 122 )CG94 - 12294 - 122
1212chain 'C' and (resid 123 through 211 )CG123 - 211123 - 212

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