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- PDB-7n6l: Crystal structure of the substrate-binding domain of E. coli DnaK... -

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Basic information

Entry
Database: PDB / ID: 7n6l
TitleCrystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide EANQQKPLLGLFADG
Components
  • Alkaline phosphatase peptide
  • Chaperone protein DnaK
KeywordsCHAPERONE/HYDROLASE / Complex / Molecular chaperone / Protein/Peptide / CHAPERONE / CHAPERONE-HYDROLASE complex
Function / homology
Function and homology information


oxidoreductase activity, acting on phosphorus or arsenic in donors / stress response to copper ion / sigma factor antagonist activity / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / chaperone cofactor-dependent protein refolding / phosphoprotein phosphatase activity / protein unfolding / cellular response to unfolded protein ...oxidoreductase activity, acting on phosphorus or arsenic in donors / stress response to copper ion / sigma factor antagonist activity / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / chaperone cofactor-dependent protein refolding / phosphoprotein phosphatase activity / protein unfolding / cellular response to unfolded protein / dephosphorylation / inclusion body / protein folding chaperone / heat shock protein binding / protein dephosphorylation / ADP binding / ATP-dependent protein folding chaperone / unfolded protein binding / outer membrane-bounded periplasmic space / response to heat / protein-folding chaperone binding / protein refolding / protein-containing complex assembly / DNA replication / periplasmic space / magnesium ion binding / ATP hydrolysis activity / protein-containing complex / zinc ion binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Chaperone DnaK / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / 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 ...Chaperone DnaK / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / 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 / Alkaline-phosphatase-like, core domain superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Alkaline phosphatase / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsJansen, R.M. / Ozden, C. / Gierasch, L.M. / Garman, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 R35 GM118161 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Selective promiscuity in the binding of E. coli Hsp70 to an unfolded protein.
Authors: Clerico, E.M. / Pozhidaeva, A.K. / Jansen, R.M. / Ozden, C. / Tilitsky, J.M. / Gierasch, L.M.
History
DepositionJun 8, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionJun 23, 2021ID: 7JMZ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 2.0Jul 14, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / entity_poly ...atom_site / entity_poly / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _entity_poly.pdbx_strand_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Oct 20, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Alkaline phosphatase peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7996
Polymers25,4232
Non-polymers3764
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-29 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.621, 95.607, 117.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-704-

SO4

21A-804-

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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dnaK, groP, grpF, seg, b0014, JW0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y8
#2: Protein/peptide Alkaline phosphatase peptide / APase


Mass: 1601.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (strain K12) (bacteria) / References: UniProt: P00634, alkaline phosphatase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 40.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.8 M (NH4)2SO4, 0.1 M K3PO4

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K throughout the collection / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Apr 14, 2020 / Details: Rigaku VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 8602 / % possible obs: 98.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.08 / Rrim(I) all: 0.186 / Χ2: 6.524 / Net I/σ(I): 8.7 / Num. measured all: 42388
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.39-2.433.22.1824060.3321.3392.5811.5792.3
2.43-2.4842.2164150.3251.2462.5571.52199.5
2.48-2.524.32.9574260.3961.5753.3651.396100
2.52-2.574.72.1234220.6051.0842.3921.533100
2.57-2.634.81.7494210.5750.8761.9631.686100
2.63-2.6951.3284530.6640.6511.4831.58599.8
2.69-2.765.10.8824030.950.4310.9852.0199.8
2.76-2.835.20.9344190.8120.451.041.888100
2.83-2.925.30.6074430.8470.2880.6742.206100
2.92-3.015.50.3824250.8820.1780.4233.295100
3.01-3.125.70.2964290.930.1350.3263.574100
3.12-3.245.60.2464260.9690.1110.2713.558100
3.24-3.395.60.2114360.9560.0960.2337.098100
3.39-3.574.50.2094050.9710.1070.2366.15895.7
3.57-3.795.30.1574490.9590.0740.17410.351100
3.79-4.094.20.1364100.9670.0720.1558.73393.2
4.09-4.54.70.1114220.9840.0540.12410.72698.4
4.5-5.155.10.1054490.990.0480.11611.92100
5.15-6.485.70.1184550.9840.0530.1317.117100
6.48-504.80.14880.9960.050.11325.00599.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DKZ

1dkz


Resolution: 2.4→47.85 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.886 / SU B: 19.944 / SU ML: 0.411 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.654 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3323 409 4.8 %RANDOM
Rwork0.2556 ---
obs0.2597 8145 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.3 Å2 / Biso mean: 53.306 Å2 / Biso min: 33.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-0 Å2
2--1.63 Å20 Å2
3----2.59 Å2
Refinement stepCycle: final / Resolution: 2.4→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 22 23 1656
Biso mean--86.55 50.31 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131643
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171542
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.6382218
X-RAY DIFFRACTIONr_angle_other_deg1.1881.5763593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9765216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75125.97272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29915292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.866155
X-RAY DIFFRACTIONr_chiral_restr0.0490.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021818
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02265
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.436 24 -
Rwork0.387 560 -
obs--92.41 %

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