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

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Basic information

Entry
Database: PDB / ID: 4jwe
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with sheep Bac7(1-21)
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 / : / protein unfolding / cellular response to unfolded protein / inclusion body / heat shock protein binding / protein folding chaperone / lipopolysaccharide binding / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / : / protein unfolding / cellular response to unfolded protein / inclusion body / heat shock protein binding / protein folding chaperone / lipopolysaccharide binding / ATP-dependent protein folding chaperone / ADP binding / antimicrobial humoral immune response mediated by antimicrobial peptide / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / protein-containing complex assembly / defense response to Gram-negative bacterium / DNA replication / defense response to Gram-positive bacterium / innate immune response / protein-containing complex / ATP hydrolysis activity / extracellular space / zinc ion binding / 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 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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)
Ovis aries (sheep)
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 / 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)53,71910
Polymers53,1424
Non-polymers5766
Water6,035335
1
A: Chaperone protein DnaK
C: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8595
Polymers26,5712
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaperone protein DnaK
D: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8595
Polymers26,5712
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Chaperone protein DnaK
D: Cathelicidin-3
hetero molecules

B: Chaperone protein DnaK
C: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,71910
Polymers53,1424
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area5550 Å2
ΔGint-90 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.659, 162.531, 44.783
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: 2750.381 Da / Num. of mol.: 2 / Fragment: unp residues 131-151 / Source method: obtained synthetically / Source: (synth.) Ovis aries (sheep) / References: UniProt: P50415
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.4 M ammonium sulfate, 0.1 M sodium acetate pH 5.0, 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: 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→24.67 Å / Num. obs: 39570 / % possible obs: 93.5 % / Biso Wilson estimate: 25.95 Å2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 0.273 / % possible all: 98.8

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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→24.67 Å / Cor.coef. Fo:Fc: 0.9354 / Cor.coef. Fo:Fc free: 0.9203 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1967 4.98 %RANDOM
Rwork0.1929 ---
obs0.1946 39514 --
Displacement parametersBiso mean: 37.15 Å2
Baniso -1Baniso -2Baniso -3
1-4.0149 Å20 Å20 Å2
2--0.0527 Å20 Å2
3----4.0676 Å2
Refine analyzeLuzzati coordinate error obs: 0.236 Å
Refinement stepCycle: LAST / Resolution: 1.95→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 30 335 3748
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013474HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14690HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1299SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes490HARMONIC5
X-RAY DIFFRACTIONt_it3474HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion18.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion480SEMIHARMONIC5
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_contact4163SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2442 138 4.65 %
Rwork0.1903 2829 -
all0.1927 2967 -
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)
11.5246-0.2554-0.20080.69280.13040.2823-0.0940.04250.11150.00370.0605-0.0063-0.0014-0.06240.0335-0.03510.00320.0020.0072-0.0184-0.0358-31.245136.6919-22.0341
24.01481.9328-0.03193.9373-2.91041.15330.00060.2808-0.0914-0.39990.5430.54420.3744-0.3069-0.5436-0.1074-0.0918-0.0803-0.07890.10490.0414-36.968419.2632-16.281
34.1826-2.9104-1.19322.1756-0.0242.8074-0.0368-0.20630.18210.06550.44960.4016-0.1052-0.5438-0.4128-0.2297-0.03910.0607-0.02290.1520.1303-55.140918.3905-3.2966
40.8383-0.0721-0.03121.52590.52310.78630.0339-0.0701-0.0973-0.0275-0.0014-0.18950.03450.0599-0.0326-0.0439-0.01860-0.02880.0113-0.0116-11.27319.0579-5.8259
56.2332.91040.14183.29431.37771.3656-0.055-0.5442-0.39130.2158-0.13430.13220.0028-0.41440.1893-0.1044-0.01170.0255-0.0130.0347-0.0099-29.947619.3632-0.3885
62.708-0.8881-2.91042.78291.8075.5828-0.00890.54420.1633-0.15640.10580.08910.1566-0.0068-0.0969-0.0859-0.152-0.01730.0071-0.0441-0.0666-21.0247-7.2046-19.1407
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|544 }A517 - 544
3X-RAY DIFFRACTION3{ A|545 - A|601 }A545 - 601
4X-RAY DIFFRACTION4{ B|389 - B|507 }B389 - 507
5X-RAY DIFFRACTION5{ B|508 - B|531 }B508 - 531
6X-RAY DIFFRACTION6{ B|532 - B|599 }B532 - 599

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