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

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Basic information

Entry
Database: PDB / ID: 4jwi
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with sheep Bac7(35-43)
Components
  • Cathelicidin-3
  • Chaperone protein DnaK
KeywordsCHAPERONE/ANTIBIOTIC / chaperone / peptide binding / antimicrobial peptide / 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 / heat shock protein binding / inclusion body / protein folding chaperone / ATP-dependent protein folding chaperone / lipopolysaccharide binding ...stress response to copper ion / sigma factor antagonist activity / : / protein unfolding / cellular response to unfolded protein / heat shock protein binding / inclusion body / protein folding chaperone / ATP-dependent protein folding chaperone / lipopolysaccharide binding / 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 / cytoplasm / cytosol
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 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Heat shock protein 70 family / Hsp70 protein / 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: 1.9 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)50,4179
Polymers49,9364
Non-polymers4805
Water6,918384
1
A: Chaperone protein DnaK
C: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1604
Polymers24,9682
Non-polymers1922
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)25,2565
Polymers24,9682
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Chaperone protein DnaK
D: Cathelicidin-3
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)50,4179
Polymers49,9364
Non-polymers4805
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area5190 Å2
ΔGint-89 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.914, 161.159, 45.114
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

21B-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: 1147.438 Da / Num. of mol.: 2 / Fragment: unp residues 165-173 / 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.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.35 %
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: Jul 27, 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→23.79 Å / Num. obs: 45783 / % possible obs: 99.9 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.065
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.414 / % possible all: 100

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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: 1.9→23.79 Å / Cor.coef. Fo:Fc: 0.9345 / Cor.coef. Fo:Fc free: 0.9106 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1420 3.11 %RANDOM
Rwork0.2006 ---
obs0.2015 45586 --
Displacement parametersBiso mean: 34.44 Å2
Baniso -1Baniso -2Baniso -3
1-5.5394 Å20 Å20 Å2
2---5.0864 Å20 Å2
3----0.453 Å2
Refine analyzeLuzzati coordinate error obs: 0.259 Å
Refinement stepCycle: LAST / Resolution: 1.9→23.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 25 384 3818
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013486HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14710HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1292SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes117HARMONIC2
X-RAY DIFFRACTIONt_gen_planes487HARMONIC5
X-RAY DIFFRACTIONt_it3486HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion17.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion485SEMIHARMONIC5
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_contact4197SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4077 112 3.38 %
Rwork0.3544 3206 -
all0.3562 3318 -
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)
11.4103-0.1310.06910.6775-0.12440.4189-0.0425-0.01190.046-0.02230.03840.0320.003-0.04240.0042-0.0757-0.00680.0045-0.0804-0.01210.0384-32.169233.1434-21.0682
20.0073-0.31760.21564.09250.74242.0485-0.0023-0.12250.08580.0472-0.0332-0.0226-0.0837-0.04040.0356-0.18870.15190.14260.0230.11270.2959-59.062726.9505-1.0169
35.8992-0.5182-2.23642.7886-0.20163.9078-0.098-0.28430.00420.29040.31150.5226-0.1873-0.5442-0.2135-0.15280.01750.058-0.03710.14170.0611-53.280416.4164-3.1242
40.799-0.3458-0.29441.25140.50750.7120.0427-0.0543-0.0407-0.0360.004-0.1807-0.02630.1077-0.0467-0.0608-0.0123-0.0103-0.07030.00640.0619-11.184318.9152-5.9587
54.43271.9113-0.19252.7110.5461.31270.0084-0.4721-0.00850.2915-0.11770.1737-0.1055-0.27670.1093-0.06410.02590.0018-0.04340.02680.0406-29.847118.9586-0.2242
64.4146-1.5386-2.5655.13382.76616.73350.00250.54420.0011-0.30190.0596-0.00850.0981-0.027-0.0622-0.14-0.1008-0.0355-0.0666-0.0688-0.0108-20.0612-8.1477-19.1229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|389 - A|542 }A389 - 542
2X-RAY DIFFRACTION2{ A|543 - A|557 }A543 - 557
3X-RAY DIFFRACTION3{ A|558 - A|601 }A558 - 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|604 }B532 - 604

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