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

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Basic information

Entry
Database: PDB / ID: 3dpq
TitleCrystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form B)
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 / 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 / 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: 2.6 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
E: Chaperone protein dnaK
F: Chaperone protein dnaK
C: inhibitor peptide
D: inhibitor peptide
G: inhibitor peptide
H: inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2479
Polymers105,1518
Non-polymers961
Water26,4101466
1
E: Chaperone protein dnaK
H: inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3843
Polymers26,2882
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-18 kcal/mol
Surface area11910 Å2
MethodPISA
2
F: Chaperone protein dnaK
G: inhibitor peptide


Theoretical massNumber of molelcules
Total (without water)26,2882
Polymers26,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-11 kcal/mol
Surface area12600 Å2
MethodPISA
3
A: Chaperone protein dnaK
D: inhibitor peptide


Theoretical massNumber of molelcules
Total (without water)26,2882
Polymers26,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-9 kcal/mol
Surface area12410 Å2
MethodPISA
4
B: Chaperone protein dnaK
C: inhibitor peptide


Theoretical massNumber of molelcules
Total (without water)26,2882
Polymers26,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-9 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.712, 91.653, 154.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 4
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: 2466.921 Da / Num. of mol.: 4 / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1466 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
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: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.893 Å / Num. obs: 27880 / % possible obs: 86.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-2.065.10.3422.153918105240.34290.4
2.06-2.185.30.23335226199030.23389.4
2.18-2.335.40.17144987892180.17189
2.33-2.525.50.135.24687485580.1388.3
2.52-2.765.50.16.54267177540.187.1
2.76-3.085.60.0817.63869169630.08185.9
3.08-3.565.50.0639.43329760620.06384.5
3.56-4.365.40.051112639848900.05180.6
4.36-6.176.10.04511.22341438410.04581.1
6.17-19.895.90.03516.71145419530.03573.2

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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 3dpo

3dpo


Resolution: 2.6→8 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.759 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.718 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.511 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.319 1354 4.9 %RANDOM
Rwork0.254 ---
obs0.257 27432 82.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 183.21 Å2 / Biso mean: 24.921 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å20 Å2
2--1.81 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 0 5 1466 8431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227014
X-RAY DIFFRACTIONr_bond_other_d0.0020.024735
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.9889472
X-RAY DIFFRACTIONr_angle_other_deg1.971311750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2485910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.13726.209306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.769151353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9791538
X-RAY DIFFRACTIONr_chiral_restr0.1030.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217752
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021158
X-RAY DIFFRACTIONr_mcbond_it3.664507
X-RAY DIFFRACTIONr_mcbond_other0.98861803
X-RAY DIFFRACTIONr_mcangle_it5.05597274
X-RAY DIFFRACTIONr_scbond_it3.78262507
X-RAY DIFFRACTIONr_scangle_it5.30792193
LS refinement shellResolution: 2.6→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.131 90 -
Rwork0.069 1833 -
all-1923 -
obs--85.5 %

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