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- PDB-1dkg: CRYSTAL STRUCTURE OF THE NUCLEOTIDE EXCHANGE FACTOR GRPE BOUND TO... -

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Basic information

Entry
Database: PDB / ID: 1dkg
TitleCRYSTAL STRUCTURE OF THE NUCLEOTIDE EXCHANGE FACTOR GRPE BOUND TO THE ATPASE DOMAIN OF THE MOLECULAR CHAPERONE DNAK
Components
  • MOLECULAR CHAPERONE DNAK
  • NUCLEOTIDE EXCHANGE FACTOR GRPE
KeywordsCOMPLEX (HSP24/HSP70) / HSP70 / GRPE / MOLECULAR CHAPERONE / NUCLEOTIDE EXCHANGE FACTOR / COILED-COIL / COMPLEX (HSP24-HSP70) / COMPLEX (HSP24-HSP70) complex
Function / homology
Function and homology information


stress response to copper ion / sigma factor antagonist activity / adenyl-nucleotide exchange factor activity / protein-containing complex disassembly / : / protein unfolding / cellular response to unfolded protein / heat shock protein binding / inclusion body / protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / adenyl-nucleotide exchange factor activity / protein-containing complex disassembly / : / 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 domain specific binding / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Nucleotide Exchange Factor Grpe; Chain A, domain 2 / Head domain of nucleotide exchange factor GrpE / GrpE nucleotide exchange factor, coiled-coil domain / GrpE nucleotide exchange factor / GrpE nucleotide exchange factor, head / GrpE nucleotide exchange factor, coiled-coil / GrpE / grpE protein signature. / Chaperone DnaK / Defensin A-like - #30 ...Nucleotide Exchange Factor Grpe; Chain A, domain 2 / Head domain of nucleotide exchange factor GrpE / GrpE nucleotide exchange factor, coiled-coil domain / GrpE nucleotide exchange factor / GrpE nucleotide exchange factor, head / GrpE nucleotide exchange factor, coiled-coil / GrpE / grpE protein signature. / Chaperone DnaK / Defensin A-like - #30 / Defensin A-like / 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 / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Hemagglutinin Ectodomain; Chain B / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chaperone protein DnaK / Protein GrpE / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsHarrison, C.J. / Kuriyan, J.
CitationJournal: Science / Year: 1997
Title: Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK.
Authors: Harrison, C.J. / Hayer-Hartl, M. / Di Liberto, M. / Hartl, F. / Kuriyan, J.
History
DepositionFeb 13, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: 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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOTIDE EXCHANGE FACTOR GRPE
B: NUCLEOTIDE EXCHANGE FACTOR GRPE
D: MOLECULAR CHAPERONE DNAK


Theoretical massNumber of molelcules
Total (without water)85,3383
Polymers85,3383
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.430, 149.430, 49.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein NUCLEOTIDE EXCHANGE FACTOR GRPE


Mass: 21882.854 Da / Num. of mol.: 2 / Mutation: CHAIN A, B, G122D
Source method: isolated from a genetically manipulated source
Details: ELASTASE PROTEOLYSIS PRODUCT, RESIDUES 34 - 197 / Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL21 (DE3) / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P09372
#2: Protein MOLECULAR CHAPERONE DNAK


Mass: 41572.105 Da / Num. of mol.: 1 / Fragment: ATPASE DOMAIN RESIDUES 3 - 383 / Mutation: CHAIN D, P319L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL21 (DE3) / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P04475, UniProt: P0A6Y8*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
23.5 %PEG80001reservoir
315 %ethylene glycol1reservoir
450 mMsodium acetate1reservoir
5190 mMlithium sulfate1reservoir
65-10 mMdithiothreitol1reservoir
710 mM(D,L)-methionine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorDetector: CCD / Date: Oct 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 26024 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 29 % / Rsym value: 0.093 / Net I/σ(I): 18
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 7 / Rsym value: 0.179 / % possible all: 86.4
Reflection
*PLUS
Num. measured all: 754420 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 86.4 % / Rmerge(I) obs: 0.179

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT CORRECTION, TORSION ANGLE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1842 7.9 %RANDOM
Rwork0.223 ---
obs0.223 23930 87.9 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5158 0 8 27 5193
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.ION
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.58

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