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- PDB-7k9v: Cryptococcus neoformans Hsp90 nucleotide binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7k9v
TitleCryptococcus neoformans Hsp90 nucleotide binding domain in complex with BUCMD00452
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
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 superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
BENZAMIDINE / Chem-W8V / Hsp90-like protein
Similarity search - Component
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2329
Polymers48,9472
Non-polymers1,2847
Water6,089338
1
A: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1625
Polymers24,4741
Non-polymers6884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0704
Polymers24,4741
Non-polymers5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.562, 44.289, 78.000
Angle α, β, γ (deg.)90.000, 104.355, 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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hsp90-like protein


Mass: 24473.609 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 345 molecules

#2: Chemical ChemComp-W8V / (1,3-dihydro-2H-isoindol-2-yl)(2,4-dihydroxy-6-{[1-methyl-3-(2-methylphenyl)-1H-pyrazol-5-yl]amino}phenyl)methanone


Mass: 440.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 M LiCl, 0.1 M Hepes or Cacodylate, 6.5 to 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-2 / Wavelength: 0.97932 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.91→29.29 Å / Num. obs: 37086 / % possible obs: 98.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.8
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3565 / CC1/2: 0.909 / % possible all: 89.5

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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: 1.91→29.29 Å / SU ML: 0.1985 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1941 1390 3.75 %
Rwork0.1639 35714 -
obs0.165 37104 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.74 Å2
Refinement stepCycle: LAST / Resolution: 1.91→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 92 338 3628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083364
X-RAY DIFFRACTIONf_angle_d0.86024548
X-RAY DIFFRACTIONf_chiral_restr0.058515
X-RAY DIFFRACTIONf_plane_restr0.0047577
X-RAY DIFFRACTIONf_dihedral_angle_d21.77511232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.980.28981360.23553369X-RAY DIFFRACTION93.89
1.98-2.060.25841410.19883542X-RAY DIFFRACTION97.67
2.06-2.150.22391280.18343526X-RAY DIFFRACTION97.73
2.15-2.260.22921350.17223532X-RAY DIFFRACTION98.1
2.26-2.40.21141220.17693591X-RAY DIFFRACTION98.28
2.4-2.590.26131350.19123603X-RAY DIFFRACTION98.42
2.59-2.850.2091490.18863567X-RAY DIFFRACTION98.67
2.85-3.260.231590.17563603X-RAY DIFFRACTION98.82
3.26-4.110.16481300.14553656X-RAY DIFFRACTION98.93
4.11-29.290.15731550.14593725X-RAY DIFFRACTION99.06
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)
16.52063952151-2.677653837410.6144682122155.01314576034-1.33034095074.59525713039-0.0986746688423-0.05980410522410.0483207117745-0.04326193411320.0931599826155-0.5912238278760.0922856362450.8052958694280.06780111032650.2773305497020.009094104070850.02435700138450.570128615191-0.01637213604530.35478078818314.508816954614.732279674120.1079784356
21.53264500855-0.6873736578980.7415435922232.337520205761.696403497086.122556715980.001379427970.241947325445-0.06311595328-0.05644613505420.04816162829610.1863262410320.155730807234-0.2820236752140.02708503514470.243935187917-0.03305239230580.01357868514120.2724418945210.06003331093530.297435491798-7.1237128589112.84097829086.40670060465
32.29756096865-0.02426287270471.203137941372.496657799272.159841227767.823519215380.173724277275-0.2875421790320.02903737510020.382338598364-0.158507519430.1284475172150.233902058123-0.8856094279860.04488809161010.361360022831-0.0109132169590.04763904939920.3856184652970.02467714484570.351905913231-8.5601146534618.810661660520.8348676313
42.99387104391-0.8143392262010.7257376200622.409030382920.6651797262164.750538246960.1276456838310.130394045593-0.4951689461360.238341102062-0.05043246876180.1114519162190.7598282510720.105682709109-0.1643754528990.43113105633-0.017949343437-0.01153217899510.253655985110.03261084024640.392103838088-0.345406274922.5629222843412.3991506503
54.349195127285.233303402850.7144051716326.279179945380.9834237529177.722999108750.136593074255-0.0144596133873-0.299904489410.1020742376090.128390984777-0.5947244262840.1517345442641.1298589586-0.2046268825370.3164754313080.106086550136-0.02403078728810.591051192041-0.006495690623860.42054668897417.26371342299.9216948502410.9598365397
62.211162095260.1844633389481.974451286484.717122806223.368247590214.62196681797-0.0855882628641.025994916191.40121328917-0.7829045799710.472822062723-0.219760096986-1.096954304680.370190952795-0.3944361157110.478084756534-0.04914401784550.04129148949460.5612188837170.07391759861950.51621048377913.99729769617.95106355427.56095721767
75.649421765832.07922888412.49647813993.029998596542.325152462072.845710555450.073232155626-0.3764539060230.2515000983960.3320672368150.0491916291731-0.07253225881730.165434600305-0.167823989199-0.07220439441390.3717743192110.0225749491159-0.0170581980220.3440664205880.0205627104910.335699607342.5135910877813.12403156320.7281478537
87.97842001047-0.0279796794123.357670439543.93672176292-1.730704827369.327694653520.141856775902-0.559133508688-0.4942621824540.3932926796130.0590359345940.5348436025321.02282514979-0.846099645298-0.3209874294390.430527864425-0.02692544489530.03888434685740.2701626700560.08981946603850.384460697187-4.622216056842.1814018985417.8451530869
93.07268715322-1.339969887151.70056221651.382606046570.4184379614385.39740406676-0.164083440287-0.672938092593-0.4346200258840.2417513014080.2279238968370.2044456096280.362018158294-0.444197995946-0.1485170763540.370584779155-0.02022387681660.05240750035810.4036615395660.09219067902220.341691445321-4.417602577917.0752651175122.3626767739
106.63543505269-2.71425629294.356267979759.19225329804-3.244292754253.20126514166-0.3392964033390.01516041460480.923971320830.2392884678460.0511684063232-0.221051970885-0.9377642565990.3470572533530.3558587907950.375734187743-0.0301620950920.02834313947970.3383098320840.006329971895170.47035082666-1.3881210486228.991065395720.4460786464
113.52373952362-2.81727903512-2.813087562389.048146672684.668155333423.324414071320.0278492110633-0.1231271257590.7047197715060.01013235566060.0465784845266-0.115359779765-0.6707505428160.375959941665-0.4910266323090.332643095908-0.00602081749134-0.01212611377180.3834592159040.01107174871180.390932281799-11.467592462225.193049712715.0199441261
122.25462951917-0.5698722110430.4250744857112.63441609436-0.7286570973453.650513315430.02543901490340.07969582265720.1500736589420.0725857652852-0.05412565175050.2099687264190.0530537300945-0.2775258794980.01016162995420.3309823217430.08447223710040.008268151639880.442659597138-0.06517983056870.315835766003-32.349064940122.158742908824.2647748763
135.00068503487-4.031509611211.09153440064.98306461814-0.2192617435922.27723141007-0.249862777789-0.643882932481-0.02376654900390.2242037644940.1930385476380.535901815287-0.312703310623-0.78883212224-0.03855704348340.3516625504690.079684072480.03694363632540.7368495722660.02165004076750.384081502836-44.434414494423.577183354528.1947053262
144.34597155413-0.423565168393-0.6090081728913.85107337405-1.037983356743.443243813510.06562083105310.3599794019080.202814210986-0.2973555789530.02213631807050.2660640105730.0893436526747-0.319942092152-0.06539666881580.309264306440.0850318654547-0.01762460129220.420132379604-0.02453999505610.244053216671-30.485527603621.870619216618.2369990689
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 26 )AA7 - 261 - 20
22chain 'A' and (resid 27 through 62 )AA27 - 6221 - 57
33chain 'A' and (resid 63 through 79 )AA63 - 7958 - 74
44chain 'A' and (resid 80 through 94 )AA80 - 9475 - 89
55chain 'A' and (resid 95 through 109 )AA95 - 10990 - 104
66chain 'A' and (resid 110 through 122 )AA110 - 122105 - 117
77chain 'A' and (resid 123 through 139 )AA123 - 139118 - 134
88chain 'A' and (resid 140 through 151 )AA140 - 151135 - 146
99chain 'A' and (resid 152 through 177 )AA152 - 177147 - 172
1010chain 'A' and (resid 178 through 197 )AA178 - 197173 - 192
1111chain 'A' and (resid 198 through 214 )AA198 - 214193 - 209
1212chain 'B' and (resid 9 through 79 )BG9 - 791 - 73
1313chain 'B' and (resid 80 through 122 )BG80 - 12274 - 116
1414chain 'B' and (resid 123 through 213 )BG123 - 213117 - 207

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