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- PDB-4r5i: Crystal structure of the DnaK C-terminus with the substrate pepti... -

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Basic information

Entry
Database: PDB / ID: 4r5i
TitleCrystal structure of the DnaK C-terminus with the substrate peptide NRLLLTG
Components
  • Chaperone protein DnaK
  • HSP70/DnaK Substrate Peptide: NRLLLTG
KeywordsCHAPERONE / Helical bundle / beta sheets / Substrate Binding / membrane
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
PHOSPHATE ION / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9702 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: HSP70/DnaK Substrate Peptide: NRLLLTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6929
Polymers26,0242
Non-polymers6687
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-53 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.243, 57.911, 180.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-851-

HOH

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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.: 1 / 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: Protein/peptide HSP70/DnaK Substrate Peptide: NRLLLTG


Mass: 786.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic (others)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.2M 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: Apr 11, 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: 1.97→45 Å / Num. all: 18325 / Num. obs: 18233 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 24.2
Reflection shellResolution: 1.97→2.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 4.2 / % possible all: 98.7

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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 / Resolution: 1.9702→41.677 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 22.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 938 5.15 %ramdom
Rwork0.1737 ---
obs0.1759 18201 99.18 %-
all-18233 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9702→41.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 35 168 1924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151762
X-RAY DIFFRACTIONf_angle_d1.5992379
X-RAY DIFFRACTIONf_dihedral_angle_d15.613661
X-RAY DIFFRACTIONf_chiral_restr0.109281
X-RAY DIFFRACTIONf_plane_restr0.007309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9702-2.07410.24641400.20512378X-RAY DIFFRACTION98
2.0741-2.20410.22261470.17822383X-RAY DIFFRACTION98
2.2041-2.37420.25751180.17162446X-RAY DIFFRACTION99
2.3742-2.61310.20611440.17182440X-RAY DIFFRACTION99
2.6131-2.99110.22431500.17132445X-RAY DIFFRACTION100
2.9911-3.76810.2041200.16322526X-RAY DIFFRACTION100
3.7681-41.6860.21191190.17692645X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.2637 Å / Origin y: -22.0449 Å / Origin z: -25.8208 Å
111213212223313233
T0.1404 Å2-0.0207 Å20.028 Å2-0.11 Å2-0.0012 Å2--0.1679 Å2
L1.7381 °2-0.7073 °20.8972 °2-1.302 °2-0.4971 °2--1.6937 °2
S-0.066 Å °-0.1685 Å °0.0908 Å °0.028 Å °0.0727 Å °0.0168 Å °-0.0659 Å °0.0244 Å °-0.0135 Å °
Refinement TLS groupSelection details: all

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