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

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Basic information

Entry
Database: PDB / ID: 4ezr
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with the C-terminal part of drosocin (residues 12 to 19)
Components
  • Chaperone protein DnaK
  • Drosocin
KeywordsCHAPERONE/PEPTIDE BINDING PROTEIN / chaperone / peptide binding / CHAPERONE-PEPTIDE BINDING PROTEIN complex
Function / homology
Function and homology information


positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / defense response to insect / stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding ...positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / defense response to insect / stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / ATP-dependent protein folding chaperone / response to bacterium / ADP binding / defense response / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / antibacterial humoral response / protein-containing complex assembly / defense response to Gram-negative bacterium / DNA replication / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / ATP hydrolysis activity / protein-containing complex / zinc ion binding / extracellular region / 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 / Drosocin antimicrobial peptides
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ENTRY 1DKZ / Resolution: 1.9 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

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Drosocin


Theoretical massNumber of molelcules
Total (without water)24,7852
Polymers24,7852
Non-polymers00
Water73941
1
A: Chaperone protein DnaK
B: Drosocin

A: Chaperone protein DnaK
B: Drosocin

A: Chaperone protein DnaK
B: Drosocin

A: Chaperone protein DnaK
B: Drosocin


Theoretical massNumber of molelcules
Total (without water)99,1408
Polymers99,1408
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 area17650 Å2
ΔGint-76 kcal/mol
Surface area36630 Å2
MethodPISA
2
A: Chaperone protein DnaK
B: Drosocin

A: Chaperone protein DnaK
B: Drosocin


Theoretical massNumber of molelcules
Total (without water)49,5704
Polymers49,5704
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area6510 Å2
ΔGint-22 kcal/mol
Surface area20630 Å2
MethodPISA
3
A: Chaperone protein DnaK
B: Drosocin

A: Chaperone protein DnaK
B: Drosocin


Theoretical massNumber of molelcules
Total (without water)49,5704
Polymers49,5704
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area4360 Å2
ΔGint-25 kcal/mol
Surface area22780 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.804, 116.433, 36.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-726-

HOH

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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: K12 / Gene: b0014, dnaK, groP, grpF, JW0013, seg / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein/peptide Drosocin


Mass: 964.146 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Drosophila melanogaster
Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P36193
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
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: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2010
RadiationMonochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 16408 / % possible obs: 99.8 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.505 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
REFMACwith PDBID 1DKZrefinement
XDSdata reduction
SCALAdata scaling
REFMACwith PDBID 1DKZphasing
RefinementMethod to determine structure: PDB ENTRY 1DKZ / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.289 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29013 829 5.1 %RANDOM
Rwork0.21606 ---
obs0.2197 15561 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.626 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---2.16 Å20 Å2
3---3.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 0 41 1769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191773
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9662396
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6395232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.1226.2282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80915341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.919159
X-RAY DIFFRACTIONr_chiral_restr0.1260.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211315
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 50 -
Rwork0.26 1035 -
obs--99.82 %
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)
16.578.85433.366412.00984.93593.9035-0.1573-0.0656-0.5215-0.2824-0.0502-0.6172-0.31940.16720.20750.16130.022-0.13020.0407-0.02750.475364.1658117.50640.6167
20.92640.18040.11811.7888-0.17320.47830.08380.05980.159-0.1014-0.03240.10480.050.0234-0.05140.0990.04030.00220.0953-0.01710.080257.483496.894630.6847
31.69720.86-0.75863.4636-0.92180.51680.1656-0.0801-0.0222-0.0286-0.2084-0.19560.03110.08560.04270.11720.039-0.01450.112-0.01030.061765.081288.785834.5657
41.44171.5479-0.28983.9211-0.32380.80970.02740.17410.6794-0.4698-0.06050.3450.0810.060.03310.1290.07810.10160.06960.13350.436455.9127106.398826.165
51.26710.73410.36246.5523-1.03731.0950.01340.0035-0.0543-0.0281-0.0483-0.16650.16140.12090.0350.0899-0.0007-0.03550.089-0.00020.068140.105474.778329.0607
62.0738-0.50350.01993.0869-1.17183.7420.06930.0178-0.11980.0646-0.0656-0.02190.20960.0124-0.00370.0871-0.0469-0.0470.1114-0.00270.054935.822277.056328.2549
715.0242-4.2263-10.3972.17215.167212.447-0.6437-0.1631-0.6142-0.1902-0.18470.3697-0.3349-0.25960.82840.25040.1288-0.05430.2096-0.0640.110556.215887.032928.6726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 395
2X-RAY DIFFRACTION2A396 - 455
3X-RAY DIFFRACTION3A456 - 495
4X-RAY DIFFRACTION4A496 - 529
5X-RAY DIFFRACTION5A530 - 566
6X-RAY DIFFRACTION6A567 - 606
7X-RAY DIFFRACTION7B12 - 19

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