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- PDB-4r5g: Crystal structure of the DnaK C-terminus with the inhibitor PET-16 -

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Basic information

Entry
Database: PDB / ID: 4r5g
TitleCrystal structure of the DnaK C-terminus with the inhibitor PET-16
ComponentsChaperone protein DnaK
KeywordsChaperone/Chaperone inhibitor / Helical bundle / beta sheets / Chaperone / HSP70/DnaK inhibitors / membrane / Chaperone-Chaperone inhibitor complex
Function / homology
Function and homology information


stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone / unfolded protein binding / response to heat / protein-folding chaperone binding / protein refolding / protein-containing complex assembly / DNA replication / ATP hydrolysis activity / protein-containing complex / zinc ion binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / 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 70 family ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / 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 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, nucleotide binding domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
triphenyl(phenylethynyl)phosphonium / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4501 Å
AuthorsLeu, J.I. / Zhang, P. / Murphy, M.E. / Marmorstein, R. / George, D.L.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Structural Basis for the Inhibition of HSP70 and DnaK Chaperones by Small-Molecule Targeting of a C-Terminal Allosteric Pocket.
Authors: Leu, J.I. / Zhang, P. / Murphy, M.E. / Marmorstein, R. / George, D.L.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8383
Polymers50,4752
Non-polymers3631
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chaperone protein DnaK

B: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8383
Polymers50,4752
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-y+1/2,x+1/2,z-1/41
Buried area3180 Å2
ΔGint-16 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.778, 91.778, 136.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsAuthors have confirmed dimer by IDT but do not know the proper assembly

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Components

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


Mass: 25237.375 Da / Num. of mol.: 2 / Fragment: C-terminus of DnaK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaK, groP, grpF, seg, b0014, JW0013 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Chemical ChemComp-3JE / triphenyl(phenylethynyl)phosphonium


Mass: 363.411 Da / Num. of mol.: 1 / Fragment: C-terminus of DnaK / Source method: obtained synthetically / Formula: C26H20P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Fragment: HSP70/DnaK inhibitor: PET-16 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.8M ammonium sulfate, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2013
RadiationMonochromator: Double silicon(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.45→45 Å / Num. all: 8306 / Num. obs: 8281 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 15
Reflection shellResolution: 3.45→3.57 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DKY

1dky


Resolution: 3.4501→43.509 Å / SU ML: 0.53 / σ(F): 1.35 / Phase error: 35.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3282 394 4.84 %random
Rwork0.2843 ---
obs0.2862 8148 99.62 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4501→43.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 27 1 2834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042859
X-RAY DIFFRACTIONf_angle_d1.0813915
X-RAY DIFFRACTIONf_dihedral_angle_d14.225899
X-RAY DIFFRACTIONf_chiral_restr0.065500
X-RAY DIFFRACTIONf_plane_restr0.005524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4501-3.9490.37581390.32496X-RAY DIFFRACTION99
3.949-4.97420.27621290.2542555X-RAY DIFFRACTION100
4.9742-43.51270.34571260.29932703X-RAY DIFFRACTION100

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