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

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Basic information

Entry
Database: PDB / ID: 3dpp
TitleCrystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)
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 / ATP-dependent protein folding chaperone / ADP binding ...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 / ATP-dependent protein folding chaperone / ADP binding / unfolded protein binding / protein-folding chaperone binding / response to heat / 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 / cytoplasm / cytosol
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 / Resolution: 2.5 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 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)52,6715
Polymers52,5754
Non-polymers961
Water5,567309
1
A: Chaperone protein dnaK
D: 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
2
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
Unit cell
Length a, b, c (Å)77.870, 159.120, 44.790
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: 2466.921 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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 46703 / Num. obs: 17463 / % possible obs: 87.7 % / Rmerge(I) obs: 0.217 / Net I/σ(I): 3.8
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 1.8 / % possible all: 93

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0073refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementStarting model: PDB entry 3dpo

3dpo


Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.871 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.878 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.975 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.316 892 5.1 %RANDOM
Rwork0.237 ---
obs0.241 17451 87.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.05 Å2 / Biso mean: 42.361 Å2 / Biso min: 18.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å20 Å2
2--1.26 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 5 309 3748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223481
X-RAY DIFFRACTIONr_bond_other_d0.0020.022300
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.9844713
X-RAY DIFFRACTIONr_angle_other_deg2.04935699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8545455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71325.946148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15215628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2041519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213873
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02582
X-RAY DIFFRACTIONr_mcbond_it1.85642273
X-RAY DIFFRACTIONr_mcbond_other0.5054908
X-RAY DIFFRACTIONr_mcangle_it2.84163650
X-RAY DIFFRACTIONr_scbond_it2.34241208
X-RAY DIFFRACTIONr_scangle_it3.56561063
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 75 -
Rwork0.308 1194 -
all-1269 -
obs--93.1 %

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