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- PDB-4f00: Crystal structure of the substrate binding domain of E.coli DnaK ... -

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Basic information

Entry
Database: PDB / ID: 4f00
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with an apidaecin fragment from the bumblebee (residues 3 to 11)
Components
  • Apidaecin
  • Chaperone protein DnaK
KeywordsCHAPERONE/IMMUNE SYSTEM / chaperone / peptide binding mode / CHAPERONE-IMMUNE SYSTEM 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 / 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
Apidaecin / Apidaecin / 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 ...Apidaecin / Apidaecin / 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 / Apidaecin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Bombus pascuorum (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ID 1DKZ / Resolution: 1.95 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: Apidaecin


Theoretical massNumber of molelcules
Total (without water)24,9712
Polymers24,9712
Non-polymers00
Water1,56787
1
A: Chaperone protein DnaK
B: Apidaecin

A: Chaperone protein DnaK
B: Apidaecin

A: Chaperone protein DnaK
B: Apidaecin

A: Chaperone protein DnaK
B: Apidaecin


Theoretical massNumber of molelcules
Total (without water)99,8858
Polymers99,8858
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 area16530 Å2
ΔGint-104 kcal/mol
Surface area37380 Å2
MethodPISA
2
A: Chaperone protein DnaK
B: Apidaecin

A: Chaperone protein DnaK
B: Apidaecin


Theoretical massNumber of molelcules
Total (without water)49,9424
Polymers49,9424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area4130 Å2
ΔGint-37 kcal/mol
Surface area22820 Å2
MethodPISA
3
A: Chaperone protein DnaK
B: Apidaecin

A: Chaperone protein DnaK
B: Apidaecin


Theoretical massNumber of molelcules
Total (without water)49,9424
Polymers49,9424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area6120 Å2
ΔGint-36 kcal/mol
Surface area20840 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-11 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.156, 116.201, 37.169
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: K-12 / Gene: b0014, dnaK, groP, grpF, JW0013, seg / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein/peptide Apidaecin


Mass: 1150.348 Da / Num. of mol.: 1 / Fragment: UNP residues 2-10 / Source method: obtained synthetically
Details: This sequence occurs naturally in bumblebees. C-terminus is amidated.
Source: (synth.) Bombus pascuorum (insect) / References: UniProt: P81464
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.4 M sodium malonate 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: 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: 1.95→25 Å / Num. obs: 15317 / % possible obs: 99.9 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.401 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
REFMACwith PDBID 1DKZrefinement
XDSdata reduction
SCALAdata scaling
REFMACwith PDBID 1DKZphasing
RefinementMethod to determine structure: PDB ID 1DKZ / Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.439 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 764 5 %RANDOM
Rwork0.19247 ---
obs0.19493 14529 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.409 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2---2.11 Å20 Å2
3---3.75 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 0 87 1809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021741
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9742351
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6645224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.83626.79578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23115328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.798157
X-RAY DIFFRACTIONr_chiral_restr0.1290.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211287
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 42 -
Rwork0.279 946 -
obs--99.7 %
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)
11.61545.64343.90521.965312.48110.2703-0.1249-0.0437-0.289-0.73670.2974-1.5451-0.4773-0.3458-0.17250.2307-0.0012-0.06230.0934-0.09610.548564.0471116.675539.5927
21.03020.2093-0.06862.1089-0.17260.350.04560.00470.0692-0.0695-0.03510.12340.01510.0207-0.01050.07140.0116-0.01290.09-0.01410.045559.32693.194331.4305
31.9232.031-0.30953.1178-0.04610.13580.0546-0.00990.20320.0042-0.00470.1366-0.01790.0238-0.050.11990.01260.0020.1005-0.00090.059265.3637101.762130.7062
41.33621.9769-0.212710.5493-1.48510.4604-0.067-0.01120.13220.001-0.0637-0.1730.0490.05030.13080.08580.0248-0.03030.1121-0.00340.090941.255882.135128.765
51.4627-0.28851.05971.0303-0.15711.79160.01130.158-0.0115-0.0518-0.02990.03180.13550.05830.01860.0762-0.0031-0.00780.1008-0.00340.027835.96376.191228.4008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 396
2X-RAY DIFFRACTION2A397 - 477
3X-RAY DIFFRACTION3A478 - 519
4X-RAY DIFFRACTION4A520 - 562
5X-RAY DIFFRACTION5A563 - 607

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