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- PDB-1hk7: Middle Domain of HSP90 -

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Basic information

Entry
Database: PDB / ID: 1hk7
TitleMiddle Domain of HSP90
ComponentsHEAT SHOCK PROTEIN HSP82Heat shock response
KeywordsCHAPERONE / HEAT SHOCK PROTEIN / ATPASE
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
Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 ...Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) 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 / MAD / Resolution: 2.5 Å
AuthorsMeyer, P. / Prodromou, C. / Roe, S.M. / Pearl, L.H.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural and Functional Analysis of the Middle Segment of Hsp90. Implications for ATP Hydrolysis and Client Protein and Cochaperone Interactions
Authors: Meyer, P. / Prodromou, C. / Hu, B. / Vaughan, C. / Roe, S.M. / Panaretou, B. / Piper, P.W. / Pearl, L.H.
History
DepositionMar 6, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN HSP82
B: HEAT SHOCK PROTEIN HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4369
Polymers67,7372
Non-polymers6997
Water3,585199
1
A: HEAT SHOCK PROTEIN HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4557
Polymers33,8681
Non-polymers5866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HEAT SHOCK PROTEIN HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9812
Polymers33,8681
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)112.879, 112.879, 112.059
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HEAT SHOCK PROTEIN HSP82 / Heat shock response / HSP90 / HSP82 / YPL240C


Mass: 33868.445 Da / Num. of mol.: 2 / Fragment: MIDDLE DOMAIN, RESIDUES 273-560
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02829
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHSP82 IS AN ESSENTIAL PROTEIN THAT IS REQUIRED BY CELLS FOR GROWTH AT HIGHER TEMPERATURES.THIS ...HSP82 IS AN ESSENTIAL PROTEIN THAT IS REQUIRED BY CELLS FOR GROWTH AT HIGHER TEMPERATURES.THIS PROTEIN IS A MOLECULAR CHAPERONE WITH ATPASE ACTIVITY. GENERALLY EXPRESSED AT LOW LEVELS BUT IS STRONGLY INDUCED AT HIGH TEMPERATURES.
Sequence detailsMIDDLE DOMAIN ONLY,RESIDUES 273-560

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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: 3.25 Å3/Da / Density % sol: 62 %
Crystal growMethod: microbatch / pH: 7.5
Details: CRYSTALS GROWN USING MICROBATCH METHOD BY MIXING 1UL OF 24MG/ML,PROTEIN IN BUFFER (20MM TRISHCL),PH 7.5, 1MM EDTA, 0.5MM DTT) WITH 1UL OF 11MM CDSO4, 20MM MGCL2, 80MM TRIS HCL, PH 7.5 AND 5% GLYCEROL.
Crystal grow
*PLUS
Temperature: 14 ℃ / pH: 7.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
124 mg/mlprotein11
211 mM11CdSO4
320 mM11MgCl2
480 mMTris-HCl11pH7.5
55 %(v/v)glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 28094 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 71.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 4.8
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.8 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.68 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1667469.42 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: LOOP A378-A384 NOT VISIBLE IN STRUCTURE. LOOP B332-B340 NOT VISIBLE IN STRUCTURE. C-TERMINUS A528-A560 NOT VISIBLE IN STRUCTURE AND C-TERMINUS B529-B560 NOT VISIBLE IN STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2655 4.8 %RANDOM
Rwork0.24 ---
obs0.24 55021 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.0687 Å2 / ksol: 0.251631 e/Å3
Displacement parametersBiso mean: 72.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.22 Å212.52 Å20 Å2
2--5.22 Å20 Å2
3----10.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 7 199 4299
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.921.5
X-RAY DIFFRACTIONc_mcangle_it3.352
X-RAY DIFFRACTIONc_scbond_it2.872
X-RAY DIFFRACTIONc_scangle_it4.162.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.413 404 4.4 %
Rwork0.387 8805 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 29.6 Å / Num. reflection obs: 26622 / Rfactor Rfree: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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