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

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Basic information

Entry
Database: PDB / ID: 4ezx
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with the designer peptide NRLMLTG
Components
  • Chaperone protein DnaK
  • synthetic peptide NRLMLTG
KeywordsCHAPERONE/PEPTIDE BINDING PROTEIN / chaperone / 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 / 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 / protein-containing complex / ATP hydrolysis activity / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
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 70kD, C-terminal domain superfamily ...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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Chaperone protein DnaK
C: synthetic peptide NRLMLTG
D: synthetic peptide NRLMLTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7329
Polymers49,2524
Non-polymers4805
Water6,071337
1
A: Chaperone protein DnaK
C: synthetic peptide NRLMLTG
hetero molecules

B: Chaperone protein DnaK
D: synthetic peptide NRLMLTG


Theoretical massNumber of molelcules
Total (without water)49,7329
Polymers49,2524
Non-polymers4805
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4440 Å2
ΔGint-102 kcal/mol
Surface area22770 Å2
MethodPISA
2
A: Chaperone protein DnaK
C: synthetic peptide NRLMLTG
hetero molecules

B: Chaperone protein DnaK
D: synthetic peptide NRLMLTG


Theoretical massNumber of molelcules
Total (without water)49,7329
Polymers49,2524
Non-polymers4805
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,-y,z+11
Buried area4980 Å2
ΔGint-87 kcal/mol
Surface area22230 Å2
MethodPISA
3
A: Chaperone protein DnaK
C: synthetic peptide NRLMLTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1067
Polymers24,6262
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-66 kcal/mol
Surface area12080 Å2
MethodPISA
4
B: Chaperone protein DnaK
D: synthetic peptide NRLMLTG


Theoretical massNumber of molelcules
Total (without water)24,6262
Polymers24,6262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.611, 149.345, 45.355
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 synthetic peptide NRLMLTG


Mass: 804.979 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.1 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: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 10, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 58626 / % possible obs: 99.6 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.439 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.417 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20856 1195 2 %RANDOM
Rwork0.17669 ---
obs0.17733 57368 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.435 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--0.15 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 25 337 3683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.023460
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2461.9824689
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1735464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38626.709158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26515672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3961516
X-RAY DIFFRACTIONr_chiral_restr0.1740.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212548
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: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 78 -
Rwork0.275 3713 -
obs--94.09 %
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)
11.25540.12970.44920.17490.10360.26520.00090.0131-0.04630.00770.01880.00380.0058-0.0139-0.01970.05520.0013-0.00330.0647-0.00820.05596.5536-33.9260.5008
25.5912-0.9893.20351.2351-0.72272.30060.06880.05330.0667-0.14580.01810.1570.0208-0.0436-0.08680.06560.0193-0.01450.03470.00980.0936-3.2804-17.6552-6.6688
35.7425-1.27893.51643.83670.95416.51740.18370.23150.1058-0.3466-0.13260.0888-0.1599-0.323-0.05110.11270.0342-0.02230.08480.05470.0722-13.0642-10.8438-15.2656
40.6394-0.06370.1070.898-0.34090.83270.058-0.0684-0.08790.0850.02750.13810.0409-0.1181-0.08550.0595-0.01670.00410.08080.03720.0618-28.532921.184-14.8269
51.09670.9924-0.42796.2702-3.462.3424-0.028-0.0415-0.2236-0.196-0.0856-0.29040.17860.1660.11360.08120.015-0.02130.06390.02730.105-14.147812.7736-12.7913
63.8137-0.1474-1.51637.1995-3.12954.985-0.1592-0.4076-0.21060.59520.47190.4239-0.0204-0.2547-0.31270.18360.07490.01470.12290.10090.1316-18.8402-6.31372.9943
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 512
2X-RAY DIFFRACTION2A513 - 558
3X-RAY DIFFRACTION3A559 - 600
4X-RAY DIFFRACTION4B389 - 508
5X-RAY DIFFRACTION5B509 - 547
6X-RAY DIFFRACTION6B548 - 599

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