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- PDB-4ezz: Crystal structure of the substrate binding domain of E.coli DnaK ... -

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Basic information

Entry
Database: PDB / ID: 4ezz
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with the designer peptide ELPLVKI
Components
  • Chaperone protein DnaK
  • synthetic peptide ELPLVKI
KeywordsCHAPERONE / peptide binding mode
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 / PDB ID 1DKZ / Resolution: 2.05 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: synthetic peptide ELPLVKI


Theoretical massNumber of molelcules
Total (without water)24,6332
Polymers24,6332
Non-polymers00
Water54030
1
A: Chaperone protein DnaK
B: synthetic peptide ELPLVKI

A: Chaperone protein DnaK
B: synthetic peptide ELPLVKI

A: Chaperone protein DnaK
B: synthetic peptide ELPLVKI

A: Chaperone protein DnaK
B: synthetic peptide ELPLVKI


Theoretical massNumber of molelcules
Total (without water)98,5318
Polymers98,5318
Non-polymers00
Water724
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 area17480 Å2
ΔGint-96 kcal/mol
Surface area37410 Å2
MethodPISA
2
A: Chaperone protein DnaK
B: synthetic peptide ELPLVKI

A: Chaperone protein DnaK
B: synthetic peptide ELPLVKI


Theoretical massNumber of molelcules
Total (without water)49,2664
Polymers49,2664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area4290 Å2
ΔGint-34 kcal/mol
Surface area23160 Å2
MethodPISA
3
A: Chaperone protein DnaK
B: synthetic peptide ELPLVKI

A: Chaperone protein DnaK
B: synthetic peptide ELPLVKI


Theoretical massNumber of molelcules
Total (without water)49,2664
Polymers49,2664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area6520 Å2
ΔGint-31 kcal/mol
Surface area20930 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-10 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.711, 116.593, 37.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 23820.777 Da / Num. of mol.: 1 / 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: Protein/peptide synthetic peptide ELPLVKI


Mass: 812.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 3.0 M ammonium sulfate, 0.1 M bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 12888 / % possible obs: 98.1 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.475 / % possible all: 94.3

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Processing

Software
NameVersionClassification
MAR345data collection
REFMACwith PDBID 1DKZrefinement
XDSdata reduction
SCALAdata scaling
REFMACwith PDBID 1DKZphasing
RefinementMethod to determine structure: PDB ID 1DKZ / Resolution: 2.05→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.882 / SU B: 13.591 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30779 624 4.8 %RANDOM
Rwork0.21751 ---
obs0.22135 12250 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.607 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2---2 Å20 Å2
3---4.13 Å2
Refinement stepCycle: LAST / Resolution: 2.05→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 0 30 1747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191736
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.9762341
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2435225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.04426.92378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9515338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.897157
X-RAY DIFFRACTIONr_chiral_restr0.1170.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211271
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 45 -
Rwork0.281 748 -
obs--88.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.09274.37254.640110.077511.000312.0980.09030.1156-0.5547-0.15840.3687-0.6035-0.28210.4267-0.4590.2407-0.0205-0.13660.16920.00940.566462.2873115.142838.1035
22.41080.55960.09781.8664-0.34020.39180.14330.05150.26-0.1543-0.1251-0.01930.050.0376-0.01820.10.04810.01570.1105-0.02190.055658.691596.823930.5302
31.844-1.38470.00675.7344-1.60752.67560.09610.0035-0.1567-0.10440.0114-0.08920.2298-0.0166-0.10760.0989-0.0176-0.08180.11090.02760.084437.481274.805328.7762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 398
2X-RAY DIFFRACTION2A399 - 533
3X-RAY DIFFRACTION3A534 - 606

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