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- PDB-1y4u: Conformation rearrangement of heat shock protein 90 upon ADP binding -

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Basic information

Entry
Database: PDB / ID: 1y4u
TitleConformation rearrangement of heat shock protein 90 upon ADP binding
ComponentsChaperone protein htpG
KeywordsCHAPERONE / Hsp90 / HtpG / molecular chaperone / ATPase
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / DNA damage response / perinuclear region of cytoplasm / protein homodimerization activity ...FtsZ-dependent cytokinesis / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / DNA damage response / perinuclear region of cytoplasm / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane / cytosol
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 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chaperone protein HtpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHuai, Q. / Wang, H. / Liu, Y. / Kim, H. / Toft, D. / Ke, H.
CitationJournal: Structure / Year: 2005
Title: Structures of the N-terminal and middle domains of E. coli Hsp90 and conformation changes upon ADP binding.
Authors: Huai, Q. / Wang, H. / Liu, Y. / Kim, H.Y. / Toft, D. / Ke, H.
History
DepositionDec 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Chaperone protein htpG
B: Chaperone protein htpG


Theoretical massNumber of molelcules
Total (without water)127,9212
Polymers127,9212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-18 kcal/mol
Surface area44280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.008, 158.008, 117.022
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Chaperone protein htpG / Heat shock protein htpG / High temperature protein G / Heat shock protein C62.5


Mass: 63960.746 Da / Num. of mol.: 2 / Fragment: residues 1-559
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: htpG / Plasmid: pBJ935 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A6Z3

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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: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6.5
Details: 1.75 M ammonium sulfate, 0.1 M MES (pH 6.5), 3% DMSO and 1 mM NaN3, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 32234 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.9
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.1 / % possible all: 87.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a monomer of the HtpG-ADP complex

Resolution: 2.9→50 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.295 -random
Rwork0.24 --
obs-30717 -
Displacement parametersBiso mean: 58.8 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7536 0 0 0 7536
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.088
X-RAY DIFFRACTIONc_angle_deg1.5

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