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- PDB-7jn9: Crystal structure of the substrate-binding domain of E. coli DnaK... -

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Basic information

Entry
Database: PDB / ID: 7jn9
TitleCrystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide QEHTGSQLRIAAYGP
Components
  • Alkaline phosphatase peptide
  • Chaperone protein DnaK
KeywordsCHAPERONE / Complex / Molecular chaperone / Protein/Peptide
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 / phosphoprotein phosphatase activity / chaperone cofactor-dependent protein refolding / 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 / phosphoprotein phosphatase activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / protein dephosphorylation / ATP-dependent protein folding chaperone / ADP binding / unfolded protein binding / protein-folding chaperone binding / outer membrane-bounded periplasmic space / response to heat / 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 / 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
DepositionAug 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 7, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / pdbx_poly_seq_scheme ...atom_site / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_2_auth_seq_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_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.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)25,6434
Polymers25,4512
Non-polymers1922
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-29 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.269, 95.610, 116.980
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-802-

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: 1629.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (strain K12) (bacteria) / References: UniProt: P00634, alkaline phosphatase
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 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: Aug 5, 2019 / 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: 2.4→50 Å / Num. obs: 8444 / % possible obs: 99.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.09 / Rrim(I) all: 0.167 / Χ2: 1.819 / Net I/σ(I): 5.2 / Num. measured all: 35881
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.4-2.443.84000.6150.7141.26797.8
2.44-2.494.14260.6540.581.23999.5
2.49-2.534.14030.6730.631.16199.5
2.53-2.594.14100.8050.51.2751000.912
2.59-2.644.24150.8030.3861.17599.50.710.812
2.64-2.74.34070.8520.3131.35799.50.5950.674
2.7-2.774.44240.9320.2711.2881000.5110.581
2.77-2.854.34240.8880.2641.3571000.4940.563
2.85-2.934.44160.9310.1761.35999.50.3380.382
2.93-3.024.54110.9270.1341.55399.80.2540.289
3.02-3.134.64180.9680.1071.56499.80.2070.234
3.13-3.264.64190.980.1143.96399.80.2230.251
3.26-3.414.54330.9760.0821.91199.50.1550.177
3.41-3.584.54140.9790.0731.96999.80.140.158
3.58-3.814.44220.980.0682.18599.80.1270.144
3.81-4.14.24330.9860.0562.18399.10.1040.118
4.1-4.524.34180.9880.0472.31699.80.0880.1
4.52-5.174.34410.9920.0452.37899.10.0860.098
5.17-6.514.14390.9870.0561.93599.10.1010.116
6.51-503.64710.9960.0352.56197.70.0590.069

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DKZ

1dkz


Resolution: 2.4→30.77 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.882 / SU B: 14.074 / SU ML: 0.309 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.613 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 404 4.8 %RANDOM
Rwork0.2238 ---
obs0.2271 8036 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.45 Å2 / Biso mean: 32.888 Å2 / Biso min: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å2-0 Å2
2--0.58 Å20 Å2
3----2.35 Å2
Refinement stepCycle: final / Resolution: 2.4→30.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 10 21 1674
Biso mean--64.58 27.39 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171556
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.642243
X-RAY DIFFRACTIONr_angle_other_deg1.2291.5813624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3075220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05625.13276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51515304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.89157
X-RAY DIFFRACTIONr_chiral_restr0.0520.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02279
LS refinement shellResolution: 2.404→2.466 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 28 -
Rwork0.292 555 -
all-583 -
obs--93.88 %

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