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- PDB-7kzu: Quasi-intermediate state (Q) of a truncated Hsp70 DnaK fused with... -

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Basic information

Entry
Database: PDB / ID: 7kzu
TitleQuasi-intermediate state (Q) of a truncated Hsp70 DnaK fused with a substrate peptide
ComponentsChaperone protein DnaK fused with substrate peptide,Chaperone 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 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / 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: 2.15 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: Acta Crystallogr.,Sect.D / Year: 2021
Title: Intermediates in allosteric equilibria of DnaK-ATP interactions with substrate peptides
Authors: Wang, W. / Hendrickson, W.A.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,4836
Polymers59,6711
Non-polymers8125
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.135, 145.135, 122.212
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-734-

HOH

21A-763-

HOH

31A-810-

HOH

41A-856-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 59671.195 Da / Num. of mol.: 1 / Fragment: Truncated (2-540),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, K-12 / 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, 162 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NaCl, 0.1 M HEPES pH 7.5, 1.6 M (NH4)2SO4

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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 PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→47.51 Å / Num. obs: 41813 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.04 / Rrim(I) all: 0.183 / Net I/σ(I): 13.4 / Num. measured all: 867680
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
2.15-2.2119.85.0046626833410.3491.1375.1340.799.5
9.12-47.5117.30.0331137665710.0080.03467.699.4

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Processing

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

4jne


Resolution: 2.15→47.51 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 1996 4.79 %
Rwork0.2057 39711 -
obs0.2074 41707 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.95 Å2 / Biso mean: 64.7254 Å2 / Biso min: 34.79 Å2
Refinement stepCycle: final / Resolution: 2.15→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 49 157 4211
Biso mean--48.18 52.5 -
Num. residues----532
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 (%)
2.15-2.20.33921370.31562740287797
2.2-2.260.3251400.305727772917100
2.26-2.330.35021400.291827832923100
2.33-2.40.29371400.264527952935100
2.4-2.490.31191410.257427942935100
2.49-2.590.27751410.243828122953100
2.59-2.710.25531410.238228062947100
2.71-2.850.27821410.242128132954100
2.85-3.030.30251430.229828272970100
3.03-3.260.25991420.227928322974100
3.26-3.590.25841440.216428663010100
3.59-4.110.21461440.179228663010100
4.11-5.180.19271470.165329163063100
5.18-47.510.21841550.182530843239100
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)
11.223-0.33780.08252.36990.25220.90010.1980.3534-0.2082-0.3717-0.25150.13440.21330.2449-00.55880.1387-0.08220.5279-0.02660.468139.866483.971126.7774
21.1426-0.65410.33291.0892-0.05931.43740.04740.1248-0.0650.0218-0.1353-0.28220.0210.485-00.45580.0407-0.04180.5420.07240.451453.57193.60837.0141
31.95540.65920.99471.09130.47450.83020.0945-0.1809-0.08790.2187-0.10610.14910.027-0.063700.46220.0062-0.01380.40280.0440.444729.921989.785545.9026
40.7858-0.69390.04231.66250.2364-0.148-0.03120.1351-0.18980.1359-0.0078-0.25360.04940.262-00.57790.1475-0.02560.66190.05250.654265.1675.883338.226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 131 )A1 - 131
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 228 )A132 - 228
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 369 )A229 - 369
4X-RAY DIFFRACTION4chain 'A' and (resid 370 through 550 )A370 - 550

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