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

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Basic information

Entry
Database: PDB / ID: 4ezt
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with heliocin (residues 14 to 21)
Components
  • Chaperone protein DnaK
  • Heliocin
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 / inclusion body / heat shock protein binding / 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 / inclusion body / heat shock protein binding / 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 / cytosol / cytoplasm
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 70 family ...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 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 / Heliocin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Heliothis virescens (tobacco budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ENTRY 1DKZ / Resolution: 2 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 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Heliocin


Theoretical massNumber of molelcules
Total (without water)25,0052
Polymers25,0052
Non-polymers00
Water64936
1
A: Chaperone protein DnaK
B: Heliocin

A: Chaperone protein DnaK
B: Heliocin

A: Chaperone protein DnaK
B: Heliocin

A: Chaperone protein DnaK
B: Heliocin


Theoretical massNumber of molelcules
Total (without water)100,0218
Polymers100,0218
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_577x,-y+2,-z+21
Buried area18220 Å2
ΔGint-87 kcal/mol
Surface area37610 Å2
MethodPISA
2
A: Chaperone protein DnaK
B: Heliocin

A: Chaperone protein DnaK
B: Heliocin


Theoretical massNumber of molelcules
Total (without water)50,0114
Polymers50,0114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area6810 Å2
ΔGint-28 kcal/mol
Surface area21100 Å2
MethodPISA
3
A: Chaperone protein DnaK
B: Heliocin

A: Chaperone protein DnaK
B: Heliocin


Theoretical massNumber of molelcules
Total (without water)50,0114
Polymers50,0114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area4870 Å2
ΔGint-27 kcal/mol
Surface area23050 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-6 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.676, 116.618, 37.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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.: 1 / Fragment: UNP residues 389-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0014, dnaK, groP, grpF, JW0013, seg / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein/peptide Heliocin


Mass: 1184.504 Da / Num. of mol.: 1 / Fragment: UNP residues 14-21 / Source method: obtained synthetically
Details: This sequence occurs naturally in Heliothis virescens. C-terminus is amidated.
Source: (synth.) Heliothis virescens (tobacco budworm) / References: UniProt: P83427
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.2 M ammonium sulfate, 0.1 M imidazole pH 7.0, 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: 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: 2→25 Å / Num. obs: 14621 / % possible obs: 99.8 % / Rmerge(I) obs: 0.036
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.387 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345data collection
REFMACwith PDBID 1DKZrefinement
XDSdata reduction
SCALAdata scaling
REFMACwith PDBID 1DKZphasing
RefinementMethod to determine structure: PDB ENTRY 1DKZ / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.591 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27075 732 5 %RANDOM
Rwork0.2201 ---
obs0.22259 13869 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.923 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2---0.58 Å20 Å2
3---1.85 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 0 36 1757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191757
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.9722372
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.6726.4281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.32715343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1861510
X-RAY DIFFRACTIONr_chiral_restr0.120.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211296
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 48 -
Rwork0.255 892 -
obs--97.92 %
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)
13.15818.10367.435922.056420.082418.3157-0.03970.0958-0.1139-0.28480.2946-0.3871-0.26450.2435-0.25490.1941-0.0313-0.03790.1624-0.01150.409263.0371115.288438.7754
21.86741.0063-0.05613.848-0.83710.93390.25050.02860.0537-0.35-0.28130.00310.08360.19990.03070.14960.1014-0.00910.1561-0.03550.089958.899893.148931.5243
33.49963.2393-0.42975.4258-0.34450.45170.254-0.10080.299-0.1238-0.39180.02160.00380.27160.13790.12490.08260.06590.27180.06290.250562.6221101.759631.4583
42.78512.7284-0.26959.9277-1.71821.2829-0.21620.1047-0.0168-0.24860.2963-0.26910.232-0.1081-0.080.1378-0.0216-0.05940.1270.01910.05340.037677.695927.7816
52.6631-0.4487-1.17876.7266-2.44952.90250.13050.3316-0.08770.1573-0.02650.18380.1571-0.1682-0.10410.2043-0.1057-0.11270.21670.06330.118334.144577.118731.591
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 398
2X-RAY DIFFRACTION2A399 - 471
3X-RAY DIFFRACTION3A472 - 526
4X-RAY DIFFRACTION4A527 - 578
5X-RAY DIFFRACTION5A579 - 605

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