[English] 日本語
Yorodumi
- PDB-1dkz: THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dkz
TitleTHE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE PEPTIDE, DETERMINED FROM TYPE 1 NATIVE CRYSTALS
Components
  • SUBSTRATE BINDING DOMAIN OF DNAK
  • SUBSTRATE PEPTIDE (7 RESIDUES)
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 / 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 / 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 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: Derived calculations / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SUBSTRATE BINDING DOMAIN OF DNAK
B: SUBSTRATE PEPTIDE (7 RESIDUES)


Theoretical massNumber of molelcules
Total (without water)24,5942
Polymers24,5942
Non-polymers00
Water4,017223
1
A: SUBSTRATE BINDING DOMAIN OF DNAK
B: SUBSTRATE PEPTIDE (7 RESIDUES)

A: SUBSTRATE BINDING DOMAIN OF DNAK
B: SUBSTRATE PEPTIDE (7 RESIDUES)


Theoretical massNumber of molelcules
Total (without water)49,1874
Polymers49,1874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area5560 Å2
ΔGint-23 kcal/mol
Surface area20840 Å2
MethodPISA, PQS
2
A: SUBSTRATE BINDING DOMAIN OF DNAK
B: SUBSTRATE PEPTIDE (7 RESIDUES)

A: SUBSTRATE BINDING DOMAIN OF DNAK
B: SUBSTRATE PEPTIDE (7 RESIDUES)

A: SUBSTRATE BINDING DOMAIN OF DNAK
B: SUBSTRATE PEPTIDE (7 RESIDUES)

A: SUBSTRATE BINDING DOMAIN OF DNAK
B: SUBSTRATE PEPTIDE (7 RESIDUES)


Theoretical massNumber of molelcules
Total (without water)98,3758
Polymers98,3758
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_577x,-y+2,-z+21
Buried area14560 Å2
ΔGint-76 kcal/mol
Surface area38240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.400, 116.700, 37.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein SUBSTRATE BINDING DOMAIN OF DNAK


Mass: 23806.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein/peptide SUBSTRATE PEPTIDE (7 RESIDUES)


Mass: 786.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.09 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

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 13127 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 37 %
Reflection
*PLUS
Num. measured all: 57907 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 60.6 % / Rmerge(I) obs: 0.143

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→5 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.274 -5 %
Rwork0.193 --
obs0.193 12016 84.7 %
Displacement parametersBiso mean: 22.5 Å2
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 0 223 1862
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.58
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
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_deg23.58
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26
X-RAY DIFFRACTIONx_mcbond_it1.3
X-RAY DIFFRACTIONx_scbond_it2.6
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scangle_it3

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more