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- PDB-1ah8: STRUCTURE OF THE ORTHORHOMBIC FORM OF THE N-TERMINAL DOMAIN OF TH... -

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Basic information

Entry
Database: PDB / ID: 1ah8
TitleSTRUCTURE OF THE ORTHORHOMBIC FORM OF THE N-TERMINAL DOMAIN OF THE YEAST HSP90 CHAPERONE
ComponentsHEAT SHOCK PROTEIN 90
KeywordsCHAPERONE / ATP-BINDING / HEAT SHOCK
Function / homology
Function and homology information


The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / protein targeting to mitochondrion ...The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsProdromou, C. / Roe, S.M. / Pearl, L.H.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: A molecular clamp in the crystal structure of the N-terminal domain of the yeast Hsp90 chaperone.
Authors: Prodromou, C. / Roe, S.M. / Piper, P.W. / Pearl, L.H.
#1: Journal: Proteins / Year: 1996
Title: Expression and Crystallization of the Yeast Hsp82 Chaperone, and Preliminary X-Ray Diffraction Studies of the Amino-Terminal Domain
Authors: Prodromou, C. / Piper, P.W. / Pearl, L.H.
History
DepositionApr 14, 1997Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN 90
B: HEAT SHOCK PROTEIN 90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1156
Polymers49,7472
Non-polymers3684
Water9,548530
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.540, 112.900, 44.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HEAT SHOCK PROTEIN 90 / HSP90


Mass: 24873.398 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02829
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSIX RESIDUE HISTIDINE TAG USED FOR PURIFICATION WAS NOT REMOVED PRIOR TO CRYSTALLISATION. IT IS NOT ...SIX RESIDUE HISTIDINE TAG USED FOR PURIFICATION WAS NOT REMOVED PRIOR TO CRYSTALLISATION. IT IS NOT SEEN IN THE STRUCTURE DETERMINATION.

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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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growMethod: under oil / pH: 5
Details: THE PROTEIN WAS CRYSTALLISED UNDER OIL IN TERASAKI PLATES. THE DROPS CONTAINED 20.5MG ML PROTEIN, 9% PEGME 550, 60MM CALCIUM CHLORIDE, 25% GLYCEROL AND 30MM SODIUM ACETATE PH 5.0, under oil
Crystal grow
*PLUS
pH: 7.4 / Method: unknown
Details: Prodromou, C., (1996) Proteins: Struct.,Funct., Genet., 25, 517.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
136 mg/mlprotein11
23 %PEGME55011
320 mM11CaCl2
410 mMTris11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: PT-COATED SI TORROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 34954 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.033 / Mean I/σ(I) obs: 7.9 / Rsym value: 0.092 / % possible all: 92.6

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Processing

Software
NameVersionClassification
TFFCmodel building
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TFFCphasing
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TETRAGONAL FORM

Resolution: 2.1→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT MODEL USED THIS IS THE ORTHORHOMBIC CRYSTAL FORM.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1705 5 %RANDOM
Rwork0.196 ---
obs0.196 33922 99 %-
Displacement parametersBiso mean: 25.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 24 530 3986
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.66
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.121
X-RAY DIFFRACTIONx_mcangle_it1.822
X-RAY DIFFRACTIONx_scbond_it2.189
X-RAY DIFFRACTIONx_scangle_it3.444
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 254 4.6 %
Rwork0.256 5271 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARWATER.TOP
X-RAY DIFFRACTION3GOL.PARGOL.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.66

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