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

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Basic information

Entry
Database: PDB / ID: 4ezy
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with the designer peptide NRLILTG
Components
  • Chaperone protein DnaK
  • synthetic peptide NRLILTG
KeywordsCHAPERONE / peptide binding mode
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 / protein-containing complex / ATP hydrolysis activity / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ID 1DKZ / Resolution: 1.85 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 / 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

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: synthetic peptide NRLILTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7043
Polymers24,6082
Non-polymers961
Water1,856103
1
A: Chaperone protein DnaK
B: synthetic peptide NRLILTG
hetero molecules

A: Chaperone protein DnaK
B: synthetic peptide NRLILTG
hetero molecules

A: Chaperone protein DnaK
B: synthetic peptide NRLILTG
hetero molecules

A: Chaperone protein DnaK
B: synthetic peptide NRLILTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,81512
Polymers98,4318
Non-polymers3844
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 area17050 Å2
ΔGint-138 kcal/mol
Surface area37830 Å2
MethodPISA
2
A: Chaperone protein DnaK
B: synthetic peptide NRLILTG
hetero molecules

A: Chaperone protein DnaK
B: synthetic peptide NRLILTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4086
Polymers49,2154
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area6280 Å2
ΔGint-55 kcal/mol
Surface area21170 Å2
MethodPISA
3
A: Chaperone protein DnaK
B: synthetic peptide NRLILTG
hetero molecules

A: Chaperone protein DnaK
B: synthetic peptide NRLILTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4086
Polymers49,2154
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area4330 Å2
ΔGint-54 kcal/mol
Surface area23110 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.435, 116.824, 37.195
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 synthetic peptide NRLILTG


Mass: 786.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3.1 M ammonium sulfate, 0.1 M MES pH 6.0, 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
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 18035 / % possible obs: 99.9 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.474 / % 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: 1.85→25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.544 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27977 920 5.1 %RANDOM
Rwork0.20152 ---
obs0.20518 17092 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: 30.653 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---1.88 Å20 Å2
3---2.42 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 5 103 1817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191742
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.9752352
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.34826.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50615338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.636158
X-RAY DIFFRACTIONr_chiral_restr0.1270.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211280
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: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 68 -
Rwork0.25 1120 -
obs--100 %
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)
15.22428.46291.192418.72175.71953.1405-0.51640.08720.0305-1.52440.44180.2665-0.66180.28490.07460.2003-0.0365-0.18370.0478-0.02550.626564.7044117.818540.8049
21.38330.14660.07382.0172-0.16160.48220.14870.02070.1645-0.1323-0.1129-0.01850.05740.0489-0.03570.13070.03560.01660.1199-0.01320.085260.106494.840131.8974
34.01390.7027-0.21885.4269-0.57130.21470.26230.16220.5599-0.1882-0.399-0.38040.03890.13750.13670.1070.05390.06810.16560.0840.266264.9216101.144729.8916
41.54141.91840.09514.3143-1.90110.79990.01650.00440.12540.0641-0.0892-0.24730.07540.0150.07270.10940.0098-0.03790.11220.00740.084542.149784.842828.8304
50.8654-0.26140.22532.6572-0.52012.90650.15790.0125-0.0755-0.1-0.0508-0.05330.2936-0.0723-0.10710.1402-0.0504-0.05360.13880.02060.084635.675775.526328.308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 395
2X-RAY DIFFRACTION2A396 - 484
3X-RAY DIFFRACTION3A485 - 517
4X-RAY DIFFRACTION4A518 - 559
5X-RAY DIFFRACTION5A560 - 607

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