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- PDB-4f01: Crystal structure of an artificial dimeric DnaK complex -

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Basic information

Entry
Database: PDB / ID: 4f01
TitleCrystal structure of an artificial dimeric DnaK complex
ComponentsChaperone protein DnaK
KeywordsCHAPERONE
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 / 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 / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZahn, M. / Straeter, N.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK.
Authors: Zahn, M. / Berthold, N. / Kieslich, B. / Knappe, D. / Hoffmann, R. / Strater, N.
History
DepositionMay 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Chaperone protein DnaK


Theoretical massNumber of molelcules
Total (without water)52,9712
Polymers52,9712
Non-polymers00
Water6,738374
1
A: Chaperone protein DnaK


Theoretical massNumber of molelcules
Total (without water)26,4861
Polymers26,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaperone protein DnaK


Theoretical massNumber of molelcules
Total (without water)26,4861
Polymers26,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-17 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.110, 61.380, 69.190
Angle α, β, γ (deg.)90.00, 103.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chaperone protein DnaK / / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70


Mass: 26485.715 Da / Num. of mol.: 2 / Fragment: UNP residues 389-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0014, dnaK, groP, grpF, JW0013, seg / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2.9 M ammonium sulfate 0.1 M MES pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2009
RadiationMonochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.39→25.14 Å / Num. obs: 97037 / % possible obs: 98.7 % / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.423 / % possible all: 98

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.98 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 1906 2 %RANDOM
Rwork0.16225 ---
obs0.16329 93091 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.3 Å2
2---0.36 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 0 374 3797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193519
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9634753
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98626.38163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71115685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7471516
X-RAY DIFFRACTIONr_chiral_restr0.1440.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212602
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr7.46233519
X-RAY DIFFRACTIONr_sphericity_free31.897591
X-RAY DIFFRACTIONr_sphericity_bonded35.52653755
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 140 -
Rwork0.266 6676 -
obs--97.73 %

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