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- PDB-2gq0: Crystal Structure of the Middle Domain of HtpG, the E. coli Hsp90 -

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Basic information

Entry
Database: PDB / ID: 2gq0
TitleCrystal Structure of the Middle Domain of HtpG, the E. coli Hsp90
ComponentsChaperone protein htpG
KeywordsChaperone / hydrolase / MOLECULAR CHAPERONE / HSP90 / HTPG / E. COLI
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
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
Chaperone protein HtpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHarris, S.F. / Shiau, A.K. / 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
DepositionApr 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)70,1172
Polymers70,1172
Non-polymers00
Water8,665481
1
A: Chaperone protein htpG


Theoretical massNumber of molelcules
Total (without water)35,0581
Polymers35,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaperone protein htpG


Theoretical massNumber of molelcules
Total (without water)35,0581
Polymers35,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.567, 149.167, 60.224
Angle α, β, γ (deg.)90.00, 99.01, 90.00
Int Tables number4
Space group name H-MP1211
DetailsHsp90 functions as a dimer, but these domains are fragments that are not connected

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Components

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


Mass: 35058.422 Da / Num. of mol.: 2 / Fragment: HTPG MIDDLE DOMAIN (230-495)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: htpG / Plasmid: PET29B / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6Z3, non-chaperonin molecular chaperone ATPase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M TRIS PH 8.5, 27-32% PEG 4000 OR PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.97959
SYNCHROTRONALS 8.2.121.0781
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 25, 2003
ADSC QUANTUM 2102CCDJan 9, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalSINGLE WAVELENGTHMx-ray1
2Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979591
21.07811
ReflectionResolution: 1.9→20 Å / Num. all: 85118 / Num. obs: 42074 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.107 / Net I/σ(I): 23
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4.9 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT1.701data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HK7

1hk7


Resolution: 1.9→19.83 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.998 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21438 2129 5.1 %RANDOM
Rwork0.17524 ---
obs0.17725 39564 96.67 %-
all-43129 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.444 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 0 481 4827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224444
X-RAY DIFFRACTIONr_bond_other_d0.0010.023060
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9496010
X-RAY DIFFRACTIONr_angle_other_deg0.92237450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7845518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93824.622238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88715820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.31528
X-RAY DIFFRACTIONr_chiral_restr0.0850.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02908
X-RAY DIFFRACTIONr_nbd_refined0.2070.2920
X-RAY DIFFRACTIONr_nbd_other0.1950.23166
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22164
X-RAY DIFFRACTIONr_nbtor_other0.0860.22265
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2381
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4021.53392
X-RAY DIFFRACTIONr_mcbond_other0.2231.51038
X-RAY DIFFRACTIONr_mcangle_it1.56424227
X-RAY DIFFRACTIONr_scbond_it2.45132189
X-RAY DIFFRACTIONr_scangle_it3.5064.51783
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 160 -
Rwork0.199 2732 -
obs--90.97 %

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