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- PDB-7kru: Stimulating state of a truncated Hsp70 DnaK fused with a substrat... -

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Basic information

Entry
Database: PDB / ID: 7kru
TitleStimulating state of a truncated Hsp70 DnaK fused with a substrate peptide
ComponentsChaperone protein DnaK fused with substrate peptide
KeywordsCHAPERONE / molecular chaperone / Hsp70 / protein folding
Function / homology
Function and homology information


unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family ...Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Alpha-Beta Complex / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 1,3-PROPANDIOL / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWang, W. / Hendrickson, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107462 United States
CitationJournal: Mol.Cell / Year: 2021
Title: Conformational equilibria in allosteric control of Hsp70 chaperones.
Authors: Wang, W. / Liu, Q. / Liu, Q. / Hendrickson, W.A.
History
DepositionNov 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Chaperone protein DnaK fused with substrate peptide
A: Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,60218
Polymers119,4312
Non-polymers2,17216
Water13,421745
1
B: Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,89910
Polymers59,7151
Non-polymers1,1849
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7038
Polymers59,7151
Non-polymers9887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.516, 98.516, 384.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-601-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 169 or resid 171...
21(chain B and (resid 2 through 169 or resid 171...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 169 or resid 171...A2 - 169
121(chain A and (resid 2 through 169 or resid 171...A171 - 229
131(chain A and (resid 2 through 169 or resid 171...A2 - 552
141(chain A and (resid 2 through 169 or resid 171...A236 - 503
151(chain A and (resid 2 through 169 or resid 171...A505 - 514
161(chain A and (resid 2 through 169 or resid 171...A516 - 517
171(chain A and (resid 2 through 169 or resid 171...A519 - 552
181(chain A and (resid 2 through 169 or resid 171...A553 - 555
211(chain B and (resid 2 through 169 or resid 171...B2 - 169
221(chain B and (resid 2 through 169 or resid 171...B171 - 229
231(chain B and (resid 2 through 169 or resid 171...B231 - 233
241(chain B and (resid 2 through 169 or resid 171...B516
251(chain B and (resid 2 through 169 or resid 171...B2 - 552
261(chain B and (resid 2 through 169 or resid 171...B547 - 552
271(chain B and (resid 2 through 169 or resid 171...B2 - 552
281(chain B and (resid 2 through 169 or resid 171...B547 - 552
291(chain B and (resid 2 through 169 or resid 171...B553 - 555

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Chaperone protein DnaK fused with substrate peptide / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70


Mass: 59715.312 Da / Num. of mol.: 2 / Fragment: Truncated (2-540) / Mutation: T199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Escherichia coli K-12 (bacteria)
Strain: K12 / Gene: dnaK, FAZ83_07380
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6D2W465

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Non-polymers , 6 types, 761 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.04 M HEPES pH 7.5, 25.5% PEG 4000, 15% glycerol, 0.17 M ammonium sulfate, 0.1M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.82→48.86 Å / Num. obs: 100002 / % possible obs: 99.9 % / Redundancy: 32.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.046 / Rrim(I) all: 0.263 / Net I/σ(I): 13.47
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 32.5 % / Rmerge(I) obs: 4.71 / Num. unique obs: 9767 / CC1/2: 0.35 / CC star: 0.72 / Rpim(I) all: 0.83 / Rrim(I) all: 4.78 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jne,1dkz

4jne

1dkz


Resolution: 1.82→48.86 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1812 1.81 %
Rwork0.1782 98126 -
obs0.1788 99938 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217.12 Å2 / Biso mean: 44.0635 Å2 / Biso min: 17.88 Å2
Refinement stepCycle: final / Resolution: 1.82→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8195 0 173 745 9113
Biso mean--55.09 43.82 -
Num. residues----1079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078481
X-RAY DIFFRACTIONf_angle_d0.83611493
X-RAY DIFFRACTIONf_dihedral_angle_d18.0043232
X-RAY DIFFRACTIONf_chiral_restr0.2081338
X-RAY DIFFRACTIONf_plane_restr0.0051507
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5018X-RAY DIFFRACTION7.064TORSIONAL
12B5018X-RAY DIFFRACTION7.064TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.82-1.870.34141360.330673387474
1.87-1.920.34961370.280974057542
1.92-1.990.27841370.24174387575
1.99-2.060.29371370.223374517588
2.06-2.140.25561380.207874467584
2.14-2.240.22431380.188374557593
2.24-2.350.23511370.176174587595
2.36-2.50.21541380.17374847622
2.5-2.70.21931400.173875277667
2.7-2.970.22931390.178275847723
2.97-3.40.1951410.166176377778
3.4-4.280.15381430.149977427885
4.28-48.860.19171510.170281618312

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