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- PDB-7kzi: Intermediate state (QQQ) of near full-length DnaK alternatively f... -

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Basic information

Entry
Database: PDB / ID: 7kzi
TitleIntermediate state (QQQ) of near full-length DnaK alternatively 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 / 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 / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)137,34211
Polymers135,8592
Non-polymers1,4839
Water1448
1
A: Chaperone protein DnaK fused with substrate peptide,Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6535
Polymers67,9291
Non-polymers7244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaperone protein DnaK fused with substrate peptide,Chaperone protein DnaK fused with substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6896
Polymers67,9291
Non-polymers7595
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.518, 121.518, 457.878
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 1 types, 2 molecules AB

#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: 67929.469 Da / Num. of mol.: 2 / Fragment: Truncated (1-609),Truncated (1-609) / 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, 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, 17 molecules

#2: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.59 Å3/Da / Density % sol: 65.75 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.5, 2.0M (NH4)2SO4, 2% PEG400, 0.15 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.82→49.75 Å / Num. obs: 48847 / % possible obs: 98.4 % / Redundancy: 36.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.024 / Rrim(I) all: 0.144 / Net I/σ(I): 18.2 / Num. measured all: 1800177 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsCC1/2% possible allRmerge(I) obsRpim(I) allRrim(I) allNet I/σ(I) obs
2.82-2.9134.213836240450.35890.8
11.28-49.7528.5272199540.99998.80.0410.0080.04276.6

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jne,1dkz

4jne

1dkz


Resolution: 2.82→49.75 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 1926 5 %
Rwork0.2552 36579 -
obs0.2561 38505 77.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.96 Å2 / Biso mean: 71.5377 Å2 / Biso min: 27.91 Å2
Refinement stepCycle: final / Resolution: 2.82→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9140 0 85 8 9233
Biso mean--57.07 43.9 -
Num. residues----1206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139320
X-RAY DIFFRACTIONf_angle_d1.8612606
X-RAY DIFFRACTIONf_dihedral_angle_d16.7423542
X-RAY DIFFRACTIONf_chiral_restr0.0991474
X-RAY DIFFRACTIONf_plane_restr0.0121660
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 (%)
2.82-2.890.4992440.484383888226
2.89-2.970.4256510.4131971102230
2.97-3.060.3289700.34811336140641
3.06-3.150.363860.3441621170749
3.16-3.270.35561020.34661943204559
3.27-3.40.45671390.3472625276479
3.4-3.550.37771720.31613283345599
3.55-3.740.3171740.299133003474100
3.74-3.970.29391760.274133403516100
3.97-4.280.2421760.24333533529100
4.28-4.710.22111770.210233763553100
4.71-5.390.22281800.212934023582100
5.39-6.790.26321840.256934843668100
6.79-49.750.21161950.198937073902100

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