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- PDB-7krw: Stimulating state of near full-length Hsp70 DnaK fused with a sub... -

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Basic information

Entry
Database: PDB / ID: 7krw
TitleStimulating state of near full-length 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 / 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, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.7 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
C: Chaperone protein DnaK fused with substrate peptide
B: Chaperone protein DnaK fused with substrate peptide
A: Chaperone protein DnaK fused with substrate peptide
D: Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,1168
Polymers269,0874
Non-polymers2,0294
Water00
1
C: Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7792
Polymers67,2721
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7792
Polymers67,2721
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7792
Polymers67,2721
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7792
Polymers67,2721
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)294.203, 294.203, 294.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 67271.812 Da / Num. of mol.: 4 / Fragment: Truncated (2-609) / 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
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
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: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7, 3.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twinOperator: -l,-k,-h / Fraction: 0.43
ReflectionResolution: 7.7→38.63 Å / Num. obs: 5107 / % possible obs: 97.1 % / Redundancy: 26.7 % / CC1/2: 0.947 / Rmerge(I) obs: 0.632 / Rpim(I) all: 0.121 / Rrim(I) all: 0.644 / Net I/σ(I): 8.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible all
7.7-7.9825.53.70.565100.410.760.743.7799.2
15.66-39.387.80.1165940.9890.0410.12392.5

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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: 7KRU

7kru


Resolution: 7.7→38.63 Å / Cross valid method: THROUGHOUT / σ(F): 5073.33 / Phase error: 54.44 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3164 263 5.24 %
Rwork0.3045 4757 -
obs0.4549 5015 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 320 Å2 / Biso mean: 320 Å2 / Biso min: 319.94 Å2
Refinement stepCycle: final / Resolution: 7.7→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16910 0 124 0 17034
Biso mean--319.97 --
Num. residues----2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917237
X-RAY DIFFRACTIONf_angle_d1.37123337
X-RAY DIFFRACTIONf_dihedral_angle_d18.2766549
X-RAY DIFFRACTIONf_chiral_restr0.0722745
X-RAY DIFFRACTIONf_plane_restr0.0083068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
7.7-9.670.56741260.52912365249194
9.69-38.630.47861320.422392252492

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