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

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Basic information

Entry
Database: PDB / ID: 4hyb
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with pyrrhocoricin_LYZI (residues 1 to 10)
Components
  • Chaperone protein DnaK
  • Pyrrhocoricin
KeywordsCHAPERONE / PEPTIDE BINDING PROTEIN / antimicrobial peptide
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 / ADP 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 / ADP binding / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / protein-containing complex assembly / DNA replication / defense response to bacterium / innate immune response / protein-containing complex / ATP hydrolysis activity / extracellular region / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 - #10 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 / Pyrrhocoricin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Pyrrhocoris apterus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ENTRY 3DPO / Resolution: 1.7 Å
AuthorsZahn, M. / Straeter, N.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK.
Authors: Zahn, M. / Berthold, N. / Kieslich, B. / Knappe, D. / Hoffmann, R. / Strater, N.
History
DepositionNov 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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: Pyrrhocoricin
D: Pyrrhocoricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5396
Polymers50,3474
Non-polymers1922
Water5,837324
1
A: Chaperone protein DnaK
C: Pyrrhocoricin


Theoretical massNumber of molelcules
Total (without water)25,1732
Polymers25,1732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-11 kcal/mol
Surface area12420 Å2
MethodPISA
2
B: Chaperone protein DnaK
D: Pyrrhocoricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3664
Polymers25,1732
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-11 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.450, 162.168, 45.208
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, b0014, JW0013 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein/peptide Pyrrhocoricin


Mass: 1352.663 Da / Num. of mol.: 2 / Fragment: UNP residues 1-10 / Source method: obtained synthetically
Details: Pyrrhocoricin sequence occurs naturally in Pyrrhocoris apterus.
Source: (synth.) Pyrrhocoris apterus (insect) / References: UniProt: P37362
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 56.37 %
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→24.6 Å / Num. obs: 60893 / % possible obs: 95.6 %
Reflection shellResolution: 1.7→1.79 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: PDB ENTRY 3DPO / Resolution: 1.7→24.6 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.09 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 3090 5.1 %RANDOM
Rwork0.21131 ---
obs0.21299 57693 95.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.194 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.49 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 10 324 3705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193464
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0651.9834683
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3695451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.97526.494154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23615660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7811516
X-RAY DIFFRACTIONr_chiral_restr0.1530.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212544
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 220 -
Rwork0.328 4312 -
obs--98.16 %
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)
11.0344-0.155-0.14380.1507-0.01230.0496-0.06430.01310.0980.00060.05550.01590.0256-0.02610.00870.0459-0.0018-0.00490.13760.00060.0712-33.048837.3053-21.7803
20.75140.3202-0.41090.9487-0.61730.7319-0.05740.04230.0002-0.01510.14650.13870.036-0.0795-0.08910.0177-0.0052-0.00990.12260.01790.0798-34.280924.3309-15.9829
37.586-1.16530.13251.0109-0.80451.7856-0.2722-0.57490.22030.08810.49570.1742-0.0516-0.4545-0.22350.01420.0390.0120.2970.10350.1309-53.968716.9371-2.9104
40.3549-0.2299-0.20310.85110.47770.40750.0264-0.078-0.0885-0.0058-0.0122-0.1374-0.04850.0497-0.01420.0355-0.0096-0.01510.12960.02130.1015-10.852118.313-5.7515
52.18191.1121-0.26991.95550.2170.27590.0419-0.12380.00620.0857-0.07380.1045-0.0418-0.01650.03190.04910.0002-0.01080.10890.00940.0399-25.947223.4611-1.9833
65.25080.4965-0.37611.9131.4831.2645-0.3021.5636-0.0006-0.02270.3265-0.01820.02730.0346-0.02440.0377-0.12510.01650.5501-0.04630.072-20.9217-7.1537-18.6348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 499
2X-RAY DIFFRACTION2A500 - 554
3X-RAY DIFFRACTION3A555 - 601
4X-RAY DIFFRACTION4B389 - 498
5X-RAY DIFFRACTION5B499 - 529
6X-RAY DIFFRACTION6B530 - 602

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