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- PDB-3c0e: Yeast Hsp82 N-terminal domain: effects of mutants 98-99 KS-AA -

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Basic information

Entry
Database: PDB / ID: 3c0e
TitleYeast Hsp82 N-terminal domain: effects of mutants 98-99 KS-AA
ComponentsATP-dependent molecular chaperone HSP82
KeywordsCHAPERONE / GRP94 / HSP82 / HSP90 / HTPG / ligand / GELDANAMYCIN / ATP-binding / Cytoplasm / Nucleotide-binding / Stress response
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsImmormino, R.M. / Gewirth, D.T.
CitationJournal: To be Published
Title: Crystal Structure of GRP94 with the Specific Mutation KS168-169AA with Bound Geldanamycin
Authors: Immormino, R.M. / Metzger IV, L.E. / Reardon, P.N. / Gewirth, D.T.
History
DepositionJan 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent molecular chaperone HSP82


Theoretical massNumber of molelcules
Total (without water)26,9711
Polymers26,9711
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.650, 73.650, 109.870
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-532-

HOH

21A-546-

HOH

31A-580-

HOH

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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: 26970.666 Da / Num. of mol.: 1 / Fragment: N-terminal Domain (Residues 1-220) / Mutation: K98A, S99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HSP82, HSP90 / Plasmid: PET15b-yHsp82(1-220) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02829
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100mM Na Succinate, 45-75 mM CaCl2, 10-15% PEG 550MME, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2007
RadiationMonochromator: sagital crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 24598 / Num. obs: 23702 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 12.1 / Net I/σ(I): 12.05
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 5.94 / Num. unique all: 2474 / Rsym value: 28.5 / % possible all: 74.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data collection
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1ZHW

1zhw


Resolution: 1.9→47.059 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 1183 5 %RANDOM
Rwork0.1707 ---
obs0.1737 23656 96.44 %-
all-24520 --
Displacement parametersBiso mean: 21.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.2733 Å20 Å20 Å2
2--0.2733 Å20 Å2
3----0.5466 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 0 378 2224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfHENIX Bonds RMSD (distance)0.007
X-RAY DIFFRACTIONfHENIX Angle RMSD (angle)1.09
X-RAY DIFFRACTIONfHENIX Chirality RMSD0.07
X-RAY DIFFRACTIONfHENIX Planarity RMSD0.004
X-RAY DIFFRACTIONfHENIX Dihedral RMSD (angle)13.855

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