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

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Basic information

Entry
Database: PDB / ID: 4jwc
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with bovine Bac7(1-16)
Components
  • Cathelicidin-3
  • Chaperone protein DnaK
KeywordsCHAPERONE/Antibiotic / chaperone / peptide binding / antimicrobial peptide / PEPTIDE BINDING PROTEIN / CHAPERONE-PROTEIN BINDING complex / 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 / protein folding chaperone / inclusion body / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone ...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 / ADP binding / ATP-dependent protein folding chaperone / unfolded protein binding / response to heat / protein-folding chaperone binding / 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
Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / 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 ...Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / 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: 1.8 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)52,0997
Polymers51,8114
Non-polymers2883
Water6,702372
1
A: Chaperone protein DnaK
C: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0013
Polymers25,9052
Non-polymers961
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)26,0974
Polymers25,9052
Non-polymers1922
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)52,0997
Polymers51,8114
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4950 Å2
ΔGint-53 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.647, 163.042, 44.770
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: uno 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: 2084.570 Da / Num. of mol.: 2 / Fragment: unp residues 131-146 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P19661
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 2.4 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: 1.8→24.68 Å / Num. obs: 53610 / % possible obs: 99.7 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.431 / % possible all: 98.5

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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: 1.8→24.67 Å / Cor.coef. Fo:Fc: 0.9397 / Cor.coef. Fo:Fc free: 0.9282 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1101 2.06 %RANDOM
Rwork0.2028 ---
obs0.2032 53476 --
Displacement parametersBiso mean: 40.05 Å2
Baniso -1Baniso -2Baniso -3
1-3.818 Å20 Å20 Å2
2---3.3079 Å20 Å2
3----0.5101 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 15 372 3773
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013506HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114746HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1318SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes502HARMONIC5
X-RAY DIFFRACTIONt_it3506HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion18.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion488SEMIHARMONIC5
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_contact4298SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 74 1.95 %
Rwork0.2061 3727 -
all0.206 3801 -
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)
11.6336-0.3469-0.1480.6790.14290.0441-0.1078-0.00210.1450.02030.06530.02240.0023-0.06490.0425-0.1120.00180.0027-0.0217-0.03150.0625-32.968937.9138-21.6031
23.82452.3289-2.6323.4745-2.91043.5827-0.03770.3423-0.0888-0.24690.45680.53850.3718-0.3405-0.4191-0.1701-0.0511-0.036-0.11910.03190.2115-30.138520.9711-19.2964
34.6895-2.9104-1.37321.3870.4223.3588-0.0071-0.26120.27480.10220.3790.4799-0.1348-0.5354-0.3719-0.304-0.03670.1218-0.13840.12380.304-54.999218.9319-3.3084
40.8935-0.2069-0.15631.62160.54140.74820.0206-0.0889-0.1044-0.04690.0197-0.14810.04520.0983-0.0404-0.0882-0.01830-0.05570.00180.082-11.572418.1745-5.3789
53.733-0.4429-0.19143.87790.78831.0146-0.0489-0.2008-0.26240.0957-0.05760.5280.0736-0.18590.1065-0.1578-0.0294-0.0313-0.10890.0283-0.0253-23.096518.8096-4.3989
60.1898-1.515-2.91040.29791.55386.64470.03620.5352-0.1334-0.1345-0.0383-0.0470.07740.14220.0022-0.2149-0.1520.01180.0154-0.1520.2242-20.6219-8.5714-20.5052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|389 - A|506 }A389 - 506
2X-RAY DIFFRACTION2{ A|507 - A|542 }A507 - 542
3X-RAY DIFFRACTION3{ A|543 - A|601 }A543 - 601
4X-RAY DIFFRACTION4{ B|389 - B|494 }B389 - 494
5X-RAY DIFFRACTION5{ B|495 - B|539 }B495 - 539
6X-RAY DIFFRACTION6{ B|540 - B|599 }B540 - 599

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