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- PDB-2akp: Hsp90 Delta24-N210 mutant -

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Basic information

Entry
Database: PDB / ID: 2akp
TitleHsp90 Delta24-N210 mutant
ComponentsATP-dependent molecular chaperone HSP82
KeywordsCHAPERONE / Hsp90 / Xray crystal structure / Intrinsic Inhibition
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
ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsRichter, K. / Moser, S. / Hagn, F. / Friedrich, R. / Hainzl, O. / Heller, M. / Schlee, S. / Kessler, H. / Reinstein, J. / Buchner, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Intrinsic inhibition of the Hsp90 ATPase activity.
Authors: Richter, K. / Moser, S. / Hagn, F. / Friedrich, R. / Hainzl, O. / Heller, M. / Schlee, S. / Kessler, H. / Reinstein, J. / Buchner, J.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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

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Assembly

Deposited unit
A: ATP-dependent molecular chaperone HSP82
B: ATP-dependent molecular chaperone HSP82


Theoretical massNumber of molelcules
Total (without water)41,9202
Polymers41,9202
Non-polymers00
Water4,486249
1
A: ATP-dependent molecular chaperone HSP82


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent molecular chaperone HSP82


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: ATP-dependent molecular chaperone HSP82

A: ATP-dependent molecular chaperone HSP82


Theoretical massNumber of molelcules
Total (without water)41,9202
Polymers41,9202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3700 Å2
ΔGint-23 kcal/mol
Surface area15600 Å2
MethodPISA, PQS
4
B: ATP-dependent molecular chaperone HSP82

B: ATP-dependent molecular chaperone HSP82


Theoretical massNumber of molelcules
Total (without water)41,9202
Polymers41,9202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)90.500, 52.950, 84.240
Angle α, β, γ (deg.)90.00, 122.05, 90.00
Int Tables number5
Space group name H-MC121

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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: 20959.877 Da / Num. of mol.: 2 / Fragment: N-terminal Delta 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HSP82, HSP90 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P02829
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→15 Å / Num. all: 25164 / Num. obs: 22195 / % possible obs: 88.2 % / Observed criterion σ(F): 2.42 / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.2 Å2
Reflection shellResolution: 1.94→2.06 Å / % possible all: 85.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1AH6

1ah6


Resolution: 1.94→14.97 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1701976.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 984 4.4 %RANDOM
Rwork0.231 ---
obs0.231 22195 88.2 %-
all-25164 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 90.6176 Å2 / ksol: 0.460409 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.64 Å20 Å22.98 Å2
2---4.14 Å20 Å2
3---0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.94→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 0 249 3145
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
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_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 68 1.9 %
Rwork0.247 3460 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION5ion.paramion.top

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