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

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Basic information

Entry
Database: PDB / ID: 4ezs
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with metchnikowin (residues 20 to 26)
Components
  • Chaperone protein DnaK
  • Metchnikowin
KeywordsCHAPERONE/PEPTIDE BINDING PROTEIN / chaperone / peptide binding / CHAPERONE-PEPTIDE BINDING PROTEIN complex
Function / homology
Function and homology information


stress response to copper ion / sigma factor antagonist activity / antifungal humoral response / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / defense response to fungus / inclusion body / protein folding chaperone / heat shock protein binding ...stress response to copper ion / sigma factor antagonist activity / antifungal humoral response / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / defense response to fungus / inclusion body / protein folding chaperone / heat shock protein binding / ADP binding / response to bacterium / ATP-dependent protein folding chaperone / defense response / response to wounding / unfolded protein binding / antibacterial humoral response / response to heat / protein-folding chaperone binding / protein refolding / protein-containing complex assembly / killing of cells of another organism / defense response to Gram-negative bacterium / DNA replication / defense response to Gram-positive 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
Metchnikowin / Metchnikowin 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 ...Metchnikowin / Metchnikowin 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 / Metchnikowin
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: To be Published
Title: Structural studies of DnaK in complex with proline rich antimicrobial peptides reveal two different peptide binding modes
Authors: Zahn, M. / Straeter, N.
History
DepositionMay 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8803
Polymers24,7842
Non-polymers961
Water1,53185
1
A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules

A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules

A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules

A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,52012
Polymers99,1368
Non-polymers3844
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 area18570 Å2
ΔGint-119 kcal/mol
Surface area36910 Å2
MethodPISA
2
A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules

A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7606
Polymers49,5684
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area6920 Å2
ΔGint-43 kcal/mol
Surface area20820 Å2
MethodPISA
3
A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules

A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7606
Polymers49,5684
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area4540 Å2
ΔGint-44 kcal/mol
Surface area23200 Å2
MethodPISA
4
A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules

A: Chaperone protein DnaK
B: Metchnikowin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7606
Polymers49,5684
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area4380 Å2
ΔGint-40 kcal/mol
Surface area23360 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-15 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.437, 116.905, 36.994
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-701-

SO4

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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 Metchnikowin /


Mass: 963.111 Da / Num. of mol.: 1 / Fragment: UNP residues 46-52 / Source method: obtained synthetically
Details: This sequence occurs naturally in Drosophila melanogaster. C-terminus is amidated.
Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q24395
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.2 M ammonium sulfate 0.1 M tris, pH 8.0, 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: Mar 4, 2011
RadiationMonochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 16552 / % possible obs: 99.7 % / Rmerge(I) obs: 0.041
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.344 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MAR345data collection
REFMACwith PDBID 1DKZrefinement
XDSdata reduction
SCALAdata scaling
REFMACwith PDBID 1DKZphasing
RefinementMethod to determine structure: PDB ENTRY 1DKZ / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.522 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25639 839 5.1 %RANDOM
Rwork0.19851 ---
obs0.20132 15682 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.882 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20 Å2
2---1.15 Å20 Å2
3---2.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 5 85 1807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191756
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.971.9742372
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.565229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44726.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89115335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.648159
X-RAY DIFFRACTIONr_chiral_restr0.1390.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211297
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
Rfree0.331 45 -
Rwork0.245 1034 -
obs--95.83 %
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)
17.129518.04859.909352.793734.280325.7309-0.38860.1045-0.4429-1.60930.3562-0.5775-1.25350.29320.03240.21670.0347-0.09340.0972-0.0180.341965.213119.206241.2621
21.42190.3088-0.18132.05-0.54450.91840.1235-0.05610.1338-0.0609-0.09520.0467-0.0120.0227-0.02830.06620.01910.00430.0683-0.02520.019160.040494.925731.7288
33.43321.0663-0.2725.0184-0.58550.17020.1186-0.01910.6323-0.0518-0.1926-0.19580.01560.09490.0740.11370.02310.0350.12810.0410.232562.2444102.422529.0235
41.02741.6976-0.015911.817-1.89571.398-0.01870.05550.12970.07580.00420.14860.15850.01810.01450.04740.0034-0.02040.0642-0.00290.045941.899781.860629.1728
52.1303-1.32490.75823.213-0.50552.47830.08210.1822-0.0144-0.07250.03760.14920.3391-0.1435-0.11960.1041-0.0493-0.03620.11660.00440.028335.566875.568827.8513
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 394
2X-RAY DIFFRACTION2A395 - 484
3X-RAY DIFFRACTION3A485 - 523
4X-RAY DIFFRACTION4A524 - 558
5X-RAY DIFFRACTION5A559 - 606

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