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- PDB-7rax: ATP-binding state of the nucleotide-binding domain of Hsp70 DnaK ... -

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Basic information

Entry
Database: PDB / ID: 7rax
TitleATP-binding state of the nucleotide-binding domain of Hsp70 DnaK mutant T199A
ComponentsChaperone protein DnaK
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, substrate binding domain, subdomain 4 ...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, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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
DepositionJul 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 9, 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
A: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2376
Polymers42,5511
Non-polymers6865
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.806, 48.118, 63.951
Angle α, β, γ (deg.)90.000, 90.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chaperone protein DnaK / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70


Mass: 42551.137 Da / Num. of mol.: 1 / Mutation: T199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (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, 473 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 277.15 K / Method: evaporation
Details: 0.1 M HEPES pH 7.5, 0.2 M sodium iodide, 20% w/v PEG 3350

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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: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.36→48.12 Å / Num. obs: 79232 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.052 / Rrim(I) all: 0.137 / Net I/σ(I): 8.1 / Num. measured all: 523261
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
1.36-1.385.72.9972206638640.2651.3383.2950.598.7
7.45-48.126.90.03437195360.9980.0140.03639.799.7

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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

4jne


Resolution: 1.41→44.18 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 1799 2.53 %
Rwork0.1636 69302 -
obs0.1642 71101 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.68 Å2 / Biso mean: 26.193 Å2 / Biso min: 9.17 Å2
Refinement stepCycle: final / Resolution: 1.41→44.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 0 60 468 3511
Biso mean--20.94 35.87 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093056
X-RAY DIFFRACTIONf_angle_d1.0234143
X-RAY DIFFRACTIONf_dihedral_angle_d16.9141157
X-RAY DIFFRACTIONf_chiral_restr0.247485
X-RAY DIFFRACTIONf_plane_restr0.006540
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.41-1.450.36991310.337652935424100
1.45-1.490.30071490.287452885437100
1.49-1.540.29141160.252353265442100
1.54-1.590.25841550.219353125467100
1.59-1.660.24691310.203953125443100
1.66-1.730.22721360.197153445480100
1.73-1.820.22211440.183453025446100
1.82-1.940.18191300.16455321545199
1.94-2.090.18331400.143153385478100
2.09-2.30.17291380.13765328546699
2.3-2.630.15871380.14215336547499
2.63-3.310.15071490.14745364551399
3.32-44.180.17721420.1495438558099
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)
10.53660.08910.16530.20560.1212-0.09-0.0060.0661-0.07380.0242-0.06460.0129-0.01760.0251-00.1805-0.01620.00950.1616-0.01940.213317.576440.427765.6774
20.2373-0.24450.36310.83090.40830.1826-0.0240.0718-0.0160.21280.01790.0098-0.0921-0.000700.1808-0.00610.00940.15830.00510.196522.062766.04383.726
30.49290.18340.20110.10740.2160.4628-0.0465-0.0595-0.0168-0.07040.0276-0.01570.0046-0.078200.2052-0.02140.00580.14670.00620.15871.244242.237372.7901
40.4230.25750.34520.34320.27330.5571-0.0182-0.06940.0412-0.03970.0334-0.0468-0.0096-0.096200.1816-0.0042-0.00940.1839-0.00270.155614.656453.2513103.5308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 1 through 39 ) or (resid 116 through 188 )) and ( bfactor > 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 115 ) and ( bfactor > 20 )A0
3X-RAY DIFFRACTION3chain 'A' and ((resid 189 through 228 ) or (resid 307 through 393)) and ( bfactor > 20 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 306 ) and ( bfactor > 20 )A0

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