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

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Basic information

Entry
Database: PDB / ID: 4ezo
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with PR-39 (residues 1 to 15)
Components
  • Antibacterial protein PR-39
  • Chaperone protein DnaK
KeywordsCHAPERONE/PEPTIDE BINDING PROTEIN / chaperone / peptide binding / CHAPERONE-PEPTIDE BINDING PROTEIN 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 / lipopolysaccharide binding / ATP-dependent protein folding chaperone ...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 / 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 / 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 / Antibacterial protein PR-39
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ENTRY 3DPO / Resolution: 1.9 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
DepositionMay 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Antibacterial protein PR-39
D: Antibacterial protein PR-39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,05310
Polymers51,4764
Non-polymers5766
Water4,504250
1
B: Chaperone protein DnaK
D: Antibacterial protein PR-39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1226
Polymers25,7382
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-9 kcal/mol
Surface area12490 Å2
MethodPISA
2
A: Chaperone protein DnaK
C: Antibacterial protein PR-39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9304
Polymers25,7382
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-9 kcal/mol
Surface area12290 Å2
MethodPISA
3
A: Chaperone protein DnaK
C: Antibacterial protein PR-39
hetero molecules

B: Chaperone protein DnaK
D: Antibacterial protein PR-39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,05310
Polymers51,4764
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4320 Å2
ΔGint-29 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.632, 161.268, 44.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: K-12 / Gene: b0014, dnaK, groP, grpF, JW0013, seg / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein/peptide Antibacterial protein PR-39


Mass: 1917.313 Da / Num. of mol.: 2 / Fragment: UNP residues 131-145 / Source method: obtained synthetically / Details: This sequence occurs naturally in pigs. / Source: (synth.) Sus scrofa (pig) / References: UniProt: P80054
#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.: 250 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.4 M ammonium sulfate, 0.1 M citric acid pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2011
RadiationMonochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→24.8 Å / Num. obs: 45171 / % possible obs: 99.9 % / Rmerge(I) obs: 0.042
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.457 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMACwith PDBID 3DPOrefinement
XDSdata reduction
SCALAdata scaling
REFMACwith PDBID 3DPOphasing
RefinementMethod to determine structure: PDB ENTRY 3DPO / Resolution: 1.9→24.8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.407 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23963 1404 3.1 %RANDOM
Rwork0.20435 ---
obs0.20552 43670 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.101 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å20 Å20 Å2
2---0.44 Å20 Å2
3---3.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3373 0 30 250 3653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023463
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0241.9854682
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.76426.234154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71715655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8441518
X-RAY DIFFRACTIONr_chiral_restr0.1460.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212538
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 111 -
Rwork0.299 2915 -
obs--99.47 %
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)
11.6336-0.3404-0.45840.21830.02330.1882-0.02850.01570.1296-0.02980.06120.01540.0178-0.059-0.03270.0621-0.0102-0.00560.0788-0.01360.0539-33.456137.1935-21.4741
22.05391.3531-0.75431.176-0.7851.2093-0.00190.02350.0666-0.03350.07040.11030.0522-0.0955-0.06850.0259-0.015-0.00530.0262-0.01240.1144-34.552923.5159-15.8468
35.3878-0.273-0.07420.6027-0.95981.9455-0.0562-0.7731-0.13520.05940.2910.2461-0.1173-0.3702-0.23480.0574-0.02820.0490.28980.09220.2026-53.679516.6254-2.592
40.6291-0.4861-0.37421.53580.59040.33590.0081-0.1101-0.0596-0.0540.0241-0.0999-0.00220.0557-0.03220.0809-0.014-0.01450.0630.00690.0503-11.191818.0744-5.5603
53.508-0.15130.3032.08880.53580.6647-0.0995-0.1319-0.0341-0.03750.08340.3729-0.0593-0.11560.01610.0560.0033-0.00620.04790.03390.0805-25.288220.4502-2.779
65.0093-0.0855-0.38823.75721.28042.1822-0.24351.1282-0.3825-0.34170.23770.13280.0063-0.10440.00580.1633-0.1532-0.00020.3432-0.13120.1842-20.005-8.5351-19.6525
79.4035-2.500223.087914.5101-4.265657.00720.0411-0.5387-0.48040.76570.80651.44410.1636-1.3104-0.84760.05630.03660.11510.1845-0.03190.4156-42.855431.976-14.458
84.1573-0.23050.71135.374-9.888233.2227-0.17480.3888-0.2114-0.15380.1825-0.01820.3527-0.2831-0.00770.0364-0.00860.00350.0523-0.0230.1015-12.64249.5735-13.2536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 501
2X-RAY DIFFRACTION2A502 - 554
3X-RAY DIFFRACTION3A555 - 599
4X-RAY DIFFRACTION4B389 - 497
5X-RAY DIFFRACTION5B498 - 534
6X-RAY DIFFRACTION6B535 - 603
7X-RAY DIFFRACTION7C5 - 12
8X-RAY DIFFRACTION8D6 - 13

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