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- PDB-2fxs: Yeast HSP82 in complex with the novel HSP90 Inhibitor Radamide -

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Basic information

Entry
Database: PDB / ID: 2fxs
TitleYeast HSP82 in complex with the novel HSP90 Inhibitor Radamide
ComponentsATP-dependent molecular chaperone HSP82
KeywordsCHAPERONE / HSP82 / HSP90 / GRP94 / HTPG / ligand / radicicol / geldanamycin / radester
Function / homology
Function and homology information


The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels ...The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / : / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-RDA / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsImmormino, R.M. / Gewirth, D.T.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Different poses for ligand and chaperone in inhibitor-bound Hsp90 and GRP94: implications for paralog-specific drug design.
Authors: Immormino, R.M. / Metzger, L.E. / Reardon, P.N. / Dollins, D.E. / Blagg, B.S. / Gewirth, D.T.
History
DepositionFeb 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 42MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. MOLPROBITY OUTPUT SCORES: ALL-ATOM CLASHSCORE : 8.38 (5.34 B<40) BAD ROTAMERS : 0.0% 0/184 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 0.0% 0/211 (TARGET 0.2%) RAMACHANDRAN FAVORED : 96.7% 204/211 (TARGET 98.0%)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent molecular chaperone HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9177
Polymers27,0451
Non-polymers8726
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.205, 74.205, 110.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-1093-

HOH

21A-1248-

HOH

DetailsThe asymmetrict unit comprises the assumed biological molecule

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Components

#1: Protein ATP-dependent molecular chaperone HSP82 / Heat shock protein Hsp90 heat-inducible isoform / 82 kDa heat shock protein


Mass: 27044.770 Da / Num. of mol.: 1 / Fragment: N-terminal Domain, Residues (1-220)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HSP82, HSP90 / Plasmid: pPET 15-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P02829
#2: Chemical ChemComp-RDA / METHYL 3-CHLORO-2-{3-[(2,5-DIHYDROXY-4-METHOXYPHENYL)AMINO]-3-OXOPROPYL}-4,6-DIHYDROXYBENZOATE


Mass: 411.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18ClNO8
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 291 K / Method: microbatch under mineral oil / pH: 5
Details: 8-9% PEG MME 550, 25% glycerol, 90 mM CaCl2 4 times as much protein as precipitant solution 1uL ligand (in DMSO) per 50 protein for final concentration ~10mM , pH 5.0, Microbatch under ...Details: 8-9% PEG MME 550, 25% glycerol, 90 mM CaCl2 4 times as much protein as precipitant solution 1uL ligand (in DMSO) per 50 protein for final concentration ~10mM , pH 5.0, Microbatch under mineral oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.99997 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 29, 2005
RadiationMonochromator: SAGITAL CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 21639 / Num. obs: 21635 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Redundancy: 14 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.069 / Net I/σ(I): 29.77
Reflection shellResolution: 2→2.05 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 5.67 / Num. unique all: 1512 / Rsym value: 0.463 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1AH6

1ah6


Resolution: 2→44.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2260080.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2119 9.8 %RANDOM
Rwork0.196 ---
all-21639 --
obs-21617 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.3372 Å2 / ksol: 0.389681 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 58 263 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 330 9.3 %
Rwork0.245 3202 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3radamide.paramradamide.top
X-RAY DIFFRACTION4gol_xplor_par.paramgol_xplor_top.top

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