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- PDB-1dky: THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE ... -

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Basic information

Entry
Database: PDB / ID: 1dky
TitleTHE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE PEPTIDE, DETERMINED FROM TYPE 2 NATIVE CRYSTALS
Components
  • DNAK
  • PEPTIDE SUBSTRATE
KeywordsCOMPLEX (MOLECULAR CHAPERONE/PEPTIDE) / DNAK / HEAT SHOCK PROTEIN 70 KDA (HSP70) / COMPLEX (MOLECULAR CHAPERONE-PEPTIDE) / COMPLEX (MOLECULAR CHAPERONE-PEPTIDE) complex
Function / homology
Function and homology information


stress response to copper ion / sigma factor antagonist activity / : / protein unfolding / cellular response to unfolded protein / heat shock protein binding / inclusion body / protein folding chaperone / ATP-dependent protein folding chaperone / ADP binding ...stress response to copper ion / sigma factor antagonist activity / : / protein unfolding / cellular response to unfolded protein / heat shock protein binding / inclusion body / protein folding chaperone / 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 / protein-containing complex / ATP hydrolysis activity / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 70kD, C-terminal domain superfamily ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsZhu, X. / Zhao, X. / Burkholder, W.F. / Gragerov, A. / Ogata, C.M. / Gottesman, M.E. / Hendrickson, W.A.
CitationJournal: Science / Year: 1996
Title: Structural analysis of substrate binding by the molecular chaperone DnaK.
Authors: Zhu, X. / Zhao, X. / Burkholder, W.F. / Gragerov, A. / Ogata, C.M. / Gottesman, M.E. / Hendrickson, W.A.
History
DepositionJun 3, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNAK
B: DNAK
C: PEPTIDE SUBSTRATE
D: PEPTIDE SUBSTRATE


Theoretical massNumber of molelcules
Total (without water)49,1874
Polymers49,1874
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-19 kcal/mol
Surface area20080 Å2
MethodPISA
2
A: DNAK
B: DNAK
C: PEPTIDE SUBSTRATE
D: PEPTIDE SUBSTRATE

A: DNAK
B: DNAK
C: PEPTIDE SUBSTRATE
D: PEPTIDE SUBSTRATE


Theoretical massNumber of molelcules
Total (without water)98,3758
Polymers98,3758
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area11650 Å2
ΔGint-64 kcal/mol
Surface area36250 Å2
MethodPISA
3
A: DNAK
C: PEPTIDE SUBSTRATE

B: DNAK
D: PEPTIDE SUBSTRATE


Theoretical massNumber of molelcules
Total (without water)49,1874
Polymers49,1874
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3300 Å2
ΔGint-27 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.400, 117.000, 36.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNAK


Mass: 23806.750 Da / Num. of mol.: 2 / Fragment: SUBSTRATE BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein/peptide PEPTIDE SUBSTRATE


Mass: 786.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 43 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: or dialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.4 Mammonium sulfate1reservoir
2phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 9117 / % possible obs: 85.2 % / Observed criterion σ(I): 2 / Redundancy: 37 %
Reflection
*PLUS
Num. measured all: 23005 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 3 Å / % possible obs: 61.6 % / Rmerge(I) obs: 0.116

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.309 -5 %
Rwork0.225 --
obs0.225 8486 79.3 %
Displacement parametersBiso mean: 30.29 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 0 28 2999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.23
X-RAY DIFFRACTIONx_mcbond_it2.5
X-RAY DIFFRACTIONx_scbond_it4.3
X-RAY DIFFRACTIONx_mcangle_it3
X-RAY DIFFRACTIONx_scangle_it5.1

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