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- PDB-2ioq: Crystal Structure of full-length HTPG, the Escherichia coli HSP90 -

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Basic information

Entry
Database: PDB / ID: 2ioq
TitleCrystal Structure of full-length HTPG, the Escherichia coli HSP90
ComponentsChaperone protein htpG
KeywordsCHAPERONE / Heat Shock Protein / Hsp90
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / response to heat / protein-folding chaperone binding / DNA damage response / ATP hydrolysis activity / protein homodimerization activity ...FtsZ-dependent cytokinesis / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / response to heat / protein-folding chaperone binding / DNA damage response / ATP hydrolysis activity / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Heat shock protein 90, C-terminal domain / 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 ...Heat shock protein 90, C-terminal domain / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chaperone protein HtpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.5 Å
AuthorsShiau, A.K. / Harris, S.F. / Agard, D.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structural Analysis of E. coli hsp90 reveals dramatic nucleotide-dependent conformational rearrangements.
Authors: Shiau, A.K. / Harris, S.F. / Southworth, D.R. / Agard, D.A.
History
DepositionOct 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Chaperone protein htpG
B: Chaperone protein htpG


Theoretical massNumber of molelcules
Total (without water)143,0392
Polymers143,0392
Non-polymers00
Water0
1
A: Chaperone protein htpG

A: Chaperone protein htpG


Theoretical massNumber of molelcules
Total (without water)143,0392
Polymers143,0392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
2
B: Chaperone protein htpG

B: Chaperone protein htpG


Theoretical massNumber of molelcules
Total (without water)143,0392
Polymers143,0392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Unit cell
Length a, b, c (Å)105.124, 105.124, 531.077
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe dimer formed by Chain A is generated by applying the operator: -y,-x,1/6. The dimer formed by Chain B is generated by applying the operator: x, x-y, 5/6.

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Components

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


Mass: 71519.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: htpG / Plasmid: pQE80 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5-10% PEG3000 or PEG4000, 30-60 mM MgCl2, 50 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2003 / Details: mirrors
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.5→58.7 Å / Num. all: 23179 / Num. obs: 22816 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 102.8 Å2 / Rsym value: 0.08 / Net I/σ(I): 21.4
Reflection shellResolution: 3.5→3.63 Å / Mean I/σ(I) obs: 2.6 / Num. unique all: 2172 / Rsym value: 0.694 / % possible all: 98.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 3.5→58.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.37 1109 -RANDOM
Rwork0.329 ---
all-23162 --
obs-22784 98.4 %-
Displacement parametersBiso mean: 120.3 Å2
Baniso -1Baniso -2Baniso -3
1-24.117 Å2-13.014 Å20 Å2
2--24.117 Å20 Å2
3----48.233 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.7 Å0.61 Å
Luzzati d res low-5 Å
Luzzati sigma a0.99 Å0.84 Å
Refinement stepCycle: LAST / Resolution: 3.5→58.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9007 0 0 0 9007
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0018
X-RAY DIFFRACTIONc_angle_deg0.684
X-RAY DIFFRACTIONc_dihedral_angle_d24.99
X-RAY DIFFRACTIONc_improper_angle_d0.496
LS refinement shellResolution: 3.5→3.63 Å
RfactorNum. reflection% reflection
Rfree0.4235 118 -
Rwork0.4114 --
obs-2097 93.5 %

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