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

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Basic information

Entry
Database: PDB / ID: 4ezw
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with the designer peptide NRLLLTG
Components
  • Chaperone protein DnaK
  • synthetic peptide NRLLLTG
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: 1.8 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
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: Chaperone protein DnaK
D: Chaperone protein DnaK
E: synthetic peptide NRLLLTG
F: synthetic peptide NRLLLTG
G: synthetic peptide NRLLLTG
H: synthetic peptide NRLLLTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,29517
Polymers98,4318
Non-polymers8659
Water11,097616
1
A: Chaperone protein DnaK
E: synthetic peptide NRLLLTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9926
Polymers24,6082
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-48 kcal/mol
Surface area12340 Å2
MethodPISA
2
B: Chaperone protein DnaK
F: synthetic peptide NRLLLTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8004
Polymers24,6082
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-30 kcal/mol
Surface area12400 Å2
MethodPISA
3
C: Chaperone protein DnaK
G: synthetic peptide NRLLLTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7043
Polymers24,6082
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-20 kcal/mol
Surface area12280 Å2
MethodPISA
4
D: Chaperone protein DnaK
H: synthetic peptide NRLLLTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8004
Polymers24,6082
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-27 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.124, 78.026, 89.482
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.: 4 / 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 NRLLLTG


Mass: 786.941 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 2.4 M ammonium sulfate, 0.1 M citric acid pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99188 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99188 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 102300 / % possible obs: 99.8 % / Rmerge(I) obs: 0.044
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.455 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→24.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.713 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22628 2044 2 %RANDOM
Rwork0.19293 ---
obs0.19361 100061 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: 31.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---2.44 Å20 Å2
3---2.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6748 0 45 616 7409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0196884
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1061.9839292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2355896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75526.688308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.128151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8761532
X-RAY DIFFRACTIONr_chiral_restr0.1580.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215020
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 141 -
Rwork0.252 7308 -
obs--99.81 %
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)
10.2464-0.32730.23551.1216-0.35570.23650.0148-0.00620.0026-0.0186-0.01270.0557-0.01750.0017-0.00210.12480.0021-0.00030.17240.01360.015841.145433.897222.0657
20.62150.04830.21092.9827-1.44461.13690.0219-0.0617-0.2769-0.0745-0.0369-0.0611-0.00130.05870.0150.1298-0.0036-0.01740.17760.02940.147547.254922.596323.4928
31.53530.2806-0.76623.6545-1.31241.43070.1780.15580.2722-0.14450.13480.1221-0.1526-0.0856-0.31280.1652-0.00730.07630.19630.04790.09658.942551.55196.9897
40.1187-0.12790.10861.3579-0.4120.22250.0047-0.0040.01910.012-0.01230.0437-0.0019-0.01870.00760.11-0.0044-0.00620.158-0.00140.018145.238831.822967.6596
50.7048-0.06910.01596.9576-4.41883.24490.08670.1063-0.09310.0123-0.00630.0259-0.063-0.0368-0.08040.0687-0.00620.00790.16250.02350.035760.633243.648358.6105
62.08250.36940.77576.345-2.5423.0644-0.10740.23080.0064-0.1130.139-0.2186-0.185-0.0252-0.03160.0992-0.02030.03290.19230.02290.024566.002353.701449.8127
71.0226-0.40070.22830.5792-0.26580.452-0.0281-0.061-0.11050.00640.0529-0.03980.02890.0215-0.02480.11460.0011-0.02410.17180.01140.038757.434210.330150.785
81.6927-0.43590.25681.6937-0.34460.65020.0092-0.13320.1653-0.0003-0.06660.0917-0.06920.01160.05750.09040.0007-0.00990.1661-0.00650.034652.356123.067449.2834
92.8495-0.37441.37092.51180.16361.71810.0731-0.0858-0.12610.29570.16770.09270.12570.0242-0.24090.10820.0059-0.03640.1869-0.02150.065882.930718.737765.405
101.384-0.23450.78110.2998-0.25330.7510.0884-0.1293-0.1166-0.0510.0059-0.00410.1289-0.0508-0.09430.1267-0.0152-0.01590.1726-0.00520.019759.870811.427596.985
110.8164-0.69650.21031.34430.18380.52160.07340.03440.2632-0.0434-0.1557-0.12520.00090.03530.08230.098-0.02210.01330.2085-0.00410.105369.558524.85998.156
122.4514-0.95971.91823.4392-1.35973.36860.1702-0.21430.2350.4741-0.1416-0.12990.12570.0899-0.02860.2279-0.0785-0.05470.295-0.02260.074189.524220.2677112.2679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 494
2X-RAY DIFFRACTION2A495 - 525
3X-RAY DIFFRACTION3A526 - 602
4X-RAY DIFFRACTION4B389 - 516
5X-RAY DIFFRACTION5B517 - 556
6X-RAY DIFFRACTION6B557 - 603
7X-RAY DIFFRACTION7C389 - 495
8X-RAY DIFFRACTION8C496 - 529
9X-RAY DIFFRACTION9C530 - 603
10X-RAY DIFFRACTION10D389 - 508
11X-RAY DIFFRACTION11D509 - 549
12X-RAY DIFFRACTION12D550 - 604

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