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

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Basic information

Entry
Database: PDB / ID: 4jwd
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with bovine Bac7(15-28)
Components
  • Cathelicidin-3
  • Chaperone protein DnaK
KeywordsCHAPERONE/Antibiotic / chaperone / peptide binding / antimicrobial peptide / PEPTIDE BINDING PROTEIN / CHAPERONE-Antibiotic complex
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 / heat shock protein binding / protein folding chaperone / ATP-dependent protein folding chaperone / ADP binding ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / heat shock protein binding / 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 / defense response to bacterium / ATP hydrolysis activity / protein-containing complex / zinc ion binding / extracellular region / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / Cystatin superfamily / Substrate Binding Domain Of DNAk; Chain A, domain 1 ...Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / Cystatin superfamily / 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 / Cathelicidin-3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsZahn, M. / Straeter, N.
CitationJournal: Protein Pept.Lett. / Year: 2014
Title: Structural Identification of DnaK Binding Sites within Bovine and Sheep Bactenecin Bac7.
Authors: Zahn, M. / Kieslich, B. / Berthold, N. / Knappe, D. / Hoffmann, R. / Strater, N.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Chaperone protein DnaK
C: Cathelicidin-3
D: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1307
Polymers50,8414
Non-polymers2883
Water5,368298
1
A: Chaperone protein DnaK
D: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5173
Polymers25,4212
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-20 kcal/mol
Surface area12300 Å2
MethodPISA
2
B: Chaperone protein DnaK
C: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6134
Polymers25,4212
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-28 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.992, 160.440, 44.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-469-

MET

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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.: 2 / Fragment: unp residues 389-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaK, groP, grpF, seg / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein/peptide Cathelicidin-3 / Bactenecin-7 / Bac7 / PR-59


Mass: 1599.941 Da / Num. of mol.: 2 / Fragment: unp residues 159-172 / Source method: obtained synthetically / Details: This sequence occurs naturally in cattles / Source: (synth.) Bos taurus (cattle) / References: UniProt: P19661
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 2.2 M ammonium sulfate, 0.1 M citric acid pH 4.4, 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: Apr 29, 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: 1.95→24.77 Å / Num. obs: 39301 / % possible obs: 93.3 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 0.534 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345data collection
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 3DPO

3dpo


Resolution: 1.95→24.77 Å / Cor.coef. Fo:Fc: 0.9411 / Cor.coef. Fo:Fc free: 0.9291 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 1982 5.05 %RANDOM
Rwork0.1873 ---
obs0.1888 39247 --
Displacement parametersBiso mean: 38.93 Å2
Baniso -1Baniso -2Baniso -3
1-6.7106 Å20 Å20 Å2
2---2.7005 Å20 Å2
3----4.0102 Å2
Refine analyzeLuzzati coordinate error obs: 0.238 Å
Refinement stepCycle: LAST / Resolution: 1.95→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 15 298 3653
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013412HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114607HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1255SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes113HARMONIC2
X-RAY DIFFRACTIONt_gen_planes479HARMONIC5
X-RAY DIFFRACTIONt_it3412HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion18.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion475SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3980SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2612 149 4.92 %
Rwork0.2148 2880 -
all0.217 3029 -
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)
11.691-0.2138-0.28150.66970.10630.4113-0.06010.01860.1006-0.02590.04990.0229-0.0004-0.0490.0102-0.0659-0.00480.0028-0.03-0.02320.0109-31.533336.1542-21.9061
27.01381.2605-0.67111.6929-1.29990.1773-0.01410.23190.1917-0.24480.23830.3860.086-0.2105-0.2242-0.1643-0.0477-0.0446-0.14340.07020.0846-40.279620.5233-13.5966
33.19310.3042-1.12391.0593-0.19112.3297-0.0617-0.34010.28490.09620.10250.4888-0.1475-0.435-0.0408-0.1586-0.01740.0474-0.00740.00870.1444-54.401617.6511-2.3268
40.9364-0.5026-0.29421.7250.61550.59790.0395-0.0844-0.0296-0.08550.0146-0.1558-0.01950.1002-0.0541-0.0532-0.025-0.0065-0.05730.00050.0103-11.411218.9367-5.9199
53.47141.590.82233.82830.91120.94520.0173-0.4632-0.21650.25-0.06570.2213-0.0406-0.33290.0484-0.0766-0.00690.0063-0.03890.02680.0497-29.269117.0309-0.9982
64.2219-1.1297-2.19436.26162.90876.9222-0.12440.54420.0122-0.48910.17220.05310.0990.0128-0.0477-0.1109-0.1162-0.0306-0.073-0.0663-0.0733-20.3541-8.4658-19.8195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|389 - A|516 }A389 - 516
2X-RAY DIFFRACTION2{ A|517 - A|550 }A517 - 550
3X-RAY DIFFRACTION3{ A|551 - A|599 }A551 - 599
4X-RAY DIFFRACTION4{ B|389 - B|507 }B389 - 507
5X-RAY DIFFRACTION5{ B|508 - B|534 }B508 - 534
6X-RAY DIFFRACTION6{ B|535 - B|602 }B535 - 602

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