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- PDB-4r5l: Crystal structure of the DnaK C-terminus (Dnak-SBD-C) -

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Basic information

Entry
Database: PDB / ID: 4r5l
TitleCrystal structure of the DnaK C-terminus (Dnak-SBD-C)
ComponentsChaperone protein DnaK
KeywordsCHAPERONE / Helical bundle / beta sheets / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9701 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: Chaperone protein DnaK
C: Chaperone protein DnaK
D: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,23518
Polymers100,9504
Non-polymers1,28614
Water39622
1
A: Chaperone protein DnaK
B: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,24110
Polymers50,4752
Non-polymers7668
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-98 kcal/mol
Surface area22230 Å2
MethodPISA
2
C: Chaperone protein DnaK
D: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9948
Polymers50,4752
Non-polymers5196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-61 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.313, 99.906, 133.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4 / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.1M 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: 2.97→45 Å / Num. all: 26253 / Num. obs: 26253 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 19.1
Reflection shellResolution: 2.97→3.08 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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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: 2.9701→41.901 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1338 5.12 %random
Rwork0.2049 ---
obs0.2069 26125 99.87 %-
all-26253 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9701→41.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6563 0 66 22 6651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046685
X-RAY DIFFRACTIONf_angle_d0.9659064
X-RAY DIFFRACTIONf_dihedral_angle_d13.9862404
X-RAY DIFFRACTIONf_chiral_restr0.0691088
X-RAY DIFFRACTIONf_plane_restr0.0031195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9701-3.07620.30831260.24922434X-RAY DIFFRACTION99
3.0762-3.19940.30671240.24992426X-RAY DIFFRACTION100
3.1994-3.34490.33251330.2392460X-RAY DIFFRACTION100
3.3449-3.52120.27481290.21872439X-RAY DIFFRACTION100
3.5212-3.74170.25321460.20242448X-RAY DIFFRACTION100
3.7417-4.03040.27731360.21472451X-RAY DIFFRACTION100
4.0304-4.43550.24181320.17222477X-RAY DIFFRACTION100
4.4355-5.07640.19091270.16612507X-RAY DIFFRACTION100
5.0764-6.39210.20491360.2252513X-RAY DIFFRACTION100
6.3921-41.9050.20411490.20042632X-RAY DIFFRACTION100

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