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- PDB-3dpo: Crystal structure of the substrate binding domain of E. coli DnaK... -

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Basic information

Entry
Database: PDB / ID: 3dpo
TitleCrystal structure of the substrate binding domain of E. coli DnaK in complex with a short pyrrhocoricin-derived inhibitor peptide
Components
  • Chaperone protein dnaK
  • inhibitor peptide
KeywordsChaperone / Peptide Binding Protein / molecular chaperone / dnaK / Hsp70 / substrate-binding domain / pyrrhocoricin inhibitor / ATP-binding / Cytoplasm / DNA replication / Membrane / Nucleotide-binding / Phosphoprotein / Stress response
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 / protein folding chaperone / inclusion body / 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 / protein folding chaperone / inclusion body / 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 / defense response to bacterium / innate immune response / ATP hydrolysis activity / protein-containing complex / zinc ion binding / extracellular region / 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
Chaperone protein DnaK / Pyrrhocoricin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsRoujeinikova, A.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Allosteric coupling between the lid and interdomain linker in DnaK revealed by inhibitor binding studies
Authors: Liebscher, M. / Roujeinikova, A.
History
DepositionJul 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: inhibitor peptide
D: inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,93110
Polymers50,3554
Non-polymers5766
Water8,935496
1
A: Chaperone protein dnaK
D: inhibitor peptide
hetero molecules

B: Chaperone protein dnaK
C: inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,93110
Polymers50,3554
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area5190 Å2
ΔGint-96 kcal/mol
Surface area22620 Å2
MethodPISA
2
A: Chaperone protein dnaK
D: inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4665
Polymers25,1772
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-44 kcal/mol
Surface area12220 Å2
MethodPISA
3
B: Chaperone protein dnaK
C: inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4665
Polymers25,1772
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-40 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.579, 159.965, 44.931
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 23820.777 Da / Num. of mol.: 2
Fragment: Substrate binding domain (UNP residues 389 to 607)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaK, groP, grpF, seg, b0014, JW0013 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y8
#2: Protein/peptide inhibitor peptide


Mass: 1356.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was pyrrhocoricin-derived. / References: UniProt: P37362*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.4 M ammonium sulfate, 100 mM citric acid, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorDate: Nov 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→69.843 Å / Num. obs: 32942 / % possible obs: 98.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.213.40.3182.31591647050.31897.9
2.21-2.353.40.2442.91501444610.24497.6
2.35-2.513.40.1913.71417141880.19197.7
2.51-2.713.40.1465.11312738960.14697.7
2.71-2.973.40.1066.91242036570.10698.1
2.97-3.323.40.0818.11121333250.08199
3.32-3.833.40.0728.61000429730.07299.3
3.83-4.73.20.04214.2812525060.04298.8
4.7-6.643.40.03616.3694420320.03699.8
6.64-80.063.20.03217.1388311990.03299.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.1data scaling
REFMAC5.4.0073refinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
PHASERphasing
RefinementStarting model: PDB entry 1dkx

1dkx


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.232 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1670 5.1 %RANDOM
Rwork0.178 ---
obs0.182 32829 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.51 Å2 / Biso mean: 22.094 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--0.53 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 30 496 4033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223579
X-RAY DIFFRACTIONr_bond_other_d0.0010.022351
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9874851
X-RAY DIFFRACTIONr_angle_other_deg1.48235839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.935469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85926.169154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6315662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2021518
X-RAY DIFFRACTIONr_chiral_restr0.0760.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023991
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02599
X-RAY DIFFRACTIONr_mcbond_it0.6441.52307
X-RAY DIFFRACTIONr_mcbond_other0.151.5924
X-RAY DIFFRACTIONr_mcangle_it1.25523718
X-RAY DIFFRACTIONr_scbond_it2.43531272
X-RAY DIFFRACTIONr_scangle_it4.2624.51133
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 122 -
Rwork0.195 2227 -
all-2349 -
obs--97.79 %

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