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

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Basic information

Entry
Database: PDB / ID: 4ezq
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with the C-terminal part of pyrrhocoricin (residues 12 to 20)
Components
  • Chaperone protein DnaK
  • Pyrrhocoricin
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 / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / ATP-dependent protein folding chaperone / ADP binding ...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 / 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 / ATP hydrolysis activity / protein-containing complex / zinc ion binding / extracellular region / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / 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 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / 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 / Pyrrhocoricin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Pyrrhocoris apterus (insect)
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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Pyrrhocoricin


Theoretical massNumber of molelcules
Total (without water)24,9492
Polymers24,9492
Non-polymers00
Water70339
1
A: Chaperone protein DnaK
B: Pyrrhocoricin

A: Chaperone protein DnaK
B: Pyrrhocoricin

A: Chaperone protein DnaK
B: Pyrrhocoricin

A: Chaperone protein DnaK
B: Pyrrhocoricin


Theoretical massNumber of molelcules
Total (without water)99,7968
Polymers99,7968
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area15680 Å2
ΔGint-79 kcal/mol
Surface area39240 Å2
MethodPISA
2
A: Chaperone protein DnaK
B: Pyrrhocoricin

A: Chaperone protein DnaK
B: Pyrrhocoricin


Theoretical massNumber of molelcules
Total (without water)49,8984
Polymers49,8984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area4320 Å2
ΔGint-30 kcal/mol
Surface area23130 Å2
MethodPISA
3
A: Chaperone protein DnaK
B: Pyrrhocoricin

A: Chaperone protein DnaK
B: Pyrrhocoricin


Theoretical massNumber of molelcules
Total (without water)49,8984
Polymers49,8984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-11
Buried area5700 Å2
ΔGint-23 kcal/mol
Surface area21750 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-8 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.620, 116.700, 38.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-728-

HOH

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


Mass: 1128.284 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Pyrrhocoris apterus
Source: (synth.) Pyrrhocoris apterus (insect) / References: UniProt: P37362
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 3.2 M ammonium sulfate, 0.1 M bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2010
RadiationMonochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 14498 / % possible obs: 98.7 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 2→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / % possible all: 96.7

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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→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.888 / SU B: 18.122 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.32075 292 2 %RANDOM
Rwork0.23545 ---
obs0.23707 14178 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.313 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2---3.16 Å20 Å2
3---4.94 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 0 39 1740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191718
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.9742316
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02626.66778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52515328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.356158
X-RAY DIFFRACTIONr_chiral_restr0.1080.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211262
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
Rfree0.345 15 -
Rwork0.334 926 -
obs--95.53 %
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)
11.7946-2.05821.38233.249-2.75092.59570.06320.1307-0.46420.307-0.25280.1376-0.44330.26130.18960.3549-0.0057-0.10140.20520.10070.5106-15.6688-2.5115-19.3326
25.6916-3.68372.06868.8306-1.51823.38850.32470.24280.493-0.2543-0.4441-0.8003-0.1402-0.16730.11930.1529-0.00760.06050.13310.06870.1297-11.2692-15.7471-16.4952
32.4381-1.31450.46178.56371.79832.18330.28970.001-0.19380.4995-0.1532-0.38440.2464-0.1776-0.13650.1436-0.0815-0.05010.16220.04780.101-12.0765-27.1438-11.2864
43.4851-5.1996-0.13918.71490.40341.02410.19140.17380.0138-0.14-0.41660.3776-0.1401-0.2530.22520.1691-0.0310.06020.2569-0.00620.2591-19.3798-15.5745-13.4331
510.0335-2.879-0.218741.14685.53240.758-0.26960.41562.7681-0.99950.3345-0.519-0.11590.12-0.0650.3846-0.0519-0.19940.4982-0.0081.11733.6291-14.536-7.7706
66.0444-7.947-1.297436.83013.80711.961-0.3741-0.0639-0.399-0.38890.40731.20030.4363-0.1236-0.03320.3081-0.0377-0.14910.2138-0.00550.15275.4487-44.2674-12.1036
73.3869-0.1711-0.93038.021.3933.256-0.0306-0.2689-0.20220.09340.09770.12570.20640.2251-0.06710.23670.0678-0.14210.2267-0.03890.112312.1351-40.4027-8.9693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 399
2X-RAY DIFFRACTION2A400 - 422
3X-RAY DIFFRACTION3A423 - 474
4X-RAY DIFFRACTION4A475 - 516
5X-RAY DIFFRACTION5A517 - 535
6X-RAY DIFFRACTION6A536 - 559
7X-RAY DIFFRACTION7A560 - 604

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