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- PDB-2iop: Crystal Structure of Full-length HtpG, the Escherichia coli Hsp90... -

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Basic information

Entry
Database: PDB / ID: 2iop
TitleCrystal Structure of Full-length HtpG, the Escherichia coli Hsp90, Bound to ADP
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 / protein-folding chaperone binding / response to heat / DNA damage response / protein homodimerization activity / ATP hydrolysis 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 / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chaperone protein HtpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Chaperone protein htpG
D: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,7868
Polymers286,0784
Non-polymers1,7094
Water00
1
A: Chaperone protein htpG
B: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8934
Polymers143,0392
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-25 kcal/mol
Surface area60460 Å2
MethodPISA
2
C: Chaperone protein htpG
D: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8934
Polymers143,0392
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-28 kcal/mol
Surface area59120 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24370 Å2
ΔGint-129 kcal/mol
Surface area102780 Å2
MethodPISA
4
A: Chaperone protein htpG
D: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8934
Polymers143,0392
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-41 kcal/mol
Surface area55760 Å2
MethodPISA
5
B: Chaperone protein htpG
C: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8934
Polymers143,0392
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-41 kcal/mol
Surface area56770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.618, 145.060, 165.352
Angle α, β, γ (deg.)90.00, 92.43, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4
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
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1-2 M Ammonium Sulfate, 0.5 M LiCl, 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 19, 2004 / 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: 3.55→46.6 Å / Num. all: 46167 / Num. obs: 36251 / % possible obs: 78.5 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 100 Å2 / Rsym value: 0.107 / Net I/σ(I): 11.8
Reflection shellResolution: 3.55→3.63 Å / Mean I/σ(I) obs: 2.3 / Num. unique all: 998 / Rsym value: 0.727 / % possible all: 32.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.55→46.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.357 2599 -RANDOM
Rwork0.317 ---
all-44882 --
obs-31922 71.1 %-
Displacement parametersBiso mean: 107.7 Å2
Baniso -1Baniso -2Baniso -3
1--13.484 Å20 Å2-12.081 Å2
2---38.399 Å20 Å2
3---51.884 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.68 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.55→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19283 0 108 0 19391
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.741
X-RAY DIFFRACTIONc_dihedral_angle_d25.98
X-RAY DIFFRACTIONc_improper_angle_d0.465
LS refinement shellResolution: 3.55→3.63 Å
RfactorNum. reflection% reflection
Rfree0.358 99 -
Rwork0.345 --
obs-1254 26 %

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