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- PDB-7krv: Stimulating state of disulfide-bridged Hsp70 DnaK -

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Basic information

Entry
Database: PDB / ID: 7krv
TitleStimulating state of disulfide-bridged Hsp70 DnaK
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
ethane-1,2-dithiol / 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: 1.92 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)121,40716
Polymers119,3872
Non-polymers2,02014
Water11,349630
1
B: Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7999
Polymers59,6931
Non-polymers1,1068
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)60,6077
Polymers59,6931
Non-polymers9146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.698, 98.698, 382.605
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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: 59693.320 Da / Num. of mol.: 2 / Fragment: Truncated (2-540) / Mutation: R167C,T199A,A480C
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 , 5 types, 644 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-6LN / ethane-1,2-dithiol


Mass: 94.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.41 %
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, 0.01 M citric acid, 3% PEG 6000

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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 EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.92→49.35 Å / Num. obs: 84808 / % possible obs: 99.8 % / Redundancy: 11.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.062 / Rrim(I) all: 0.209 / Net I/σ(I): 7.7 / Num. measured all: 937591 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.92-1.9610.34.2554370142400.3231.3584.4740.596.3
10.18-49.359.50.037683371710.0120.03934.199.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KRU

7kru


Resolution: 1.92→49.35 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 1997 2.36 %
Rwork0.189 82595 -
obs0.19 84592 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.34 Å2 / Biso mean: 46.6858 Å2 / Biso min: 19.6 Å2
Refinement stepCycle: final / Resolution: 1.92→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8187 0 142 630 8959
Biso mean--50.1 42.48 -
Num. residues----1079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128462
X-RAY DIFFRACTIONf_angle_d1.15511470
X-RAY DIFFRACTIONf_dihedral_angle_d17.8423222
X-RAY DIFFRACTIONf_chiral_restr0.2131338
X-RAY DIFFRACTIONf_plane_restr0.0081505
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.970.34021360.33895579571596
1.97-2.020.37811390.290957955934100
2.02-2.080.30511410.267158095950100
2.08-2.150.3221410.24758245965100
2.15-2.230.31221400.236957985938100
2.23-2.320.2751420.225558435985100
2.32-2.420.29371410.214458365977100
2.42-2.550.26171420.201158706012100
2.55-2.710.19681420.184958856027100
2.71-2.920.26281420.195559176059100
2.92-3.210.27591450.191659496094100
3.21-3.680.23441440.169459836127100
3.68-4.630.16791470.144760696216100
4.63-49.350.19621550.17666438659399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38570.21420.34890.971-0.16180.65960.09660.02750.0598-0.0111-0.0150.31750.13340.1472-00.1901-0.01890.04180.1426-0.03040.22335.48839.5008175.5674
20.15280.05770.11710.9281-0.31670.0966-0.00180.0113-0.00980.03370.0087-0.03970.02150.0154-00.1974-0.00110.01470.1948-0.01820.168355.700340.6177173.364
30.207-0.0020.1170.0241-0.03510.34610.02590.04980.03190.0087-0.02320.0610.00260.006300.20180.0165-0.00880.2684-0.02520.254736.82562.4011146.4064
40.5573-0.3829-0.01680.76630.07680.44620.0084-0.00450.00580.01710.0223-0.06450.0440.050200.17830.0328-0.0210.2009-0.01910.186161.479839.1371203.5588
50.0644-0.1386-0.04421.03450.28060.29060.00610.0399-0.02510.0234-0.05450.08840.0054-0.0382-00.16190.0142-0.00890.1485-0.03160.162641.56840.5668206.2582
60.30680.14370.34840.1084-0.02790.51590.0464-0.0444-0.00550.0349-0.0014-0.0370.0022-0.014700.20010.0022-0.02910.2122-0.02790.207360.822162.9319232.6107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 163 )B2 - 163
2X-RAY DIFFRACTION2chain 'B' and (resid 164 through 369 )B164 - 369
3X-RAY DIFFRACTION3chain 'B' and (resid 370 through 552 )B370 - 552
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 163 )A2 - 163
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 369 )A164 - 369
6X-RAY DIFFRACTION6chain 'A' and (resid 370 through 552 )A370 - 552

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