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- PDB-7n6m: Crystal structure of the substrate-binding domain of E. coli DnaK... -

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Basic information

Entry
Database: PDB / ID: 7n6m
TitleCrystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide RQKPLLGLSR
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 / : / 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 / : / phosphoprotein phosphatase activity / protein unfolding / cellular response to unfolded protein / protein dephosphorylation / heat shock protein binding / inclusion body / protein folding chaperone / 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 / periplasmic space / DNA replication / magnesium ion binding / 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 / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / 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 / Alkaline-phosphatase-like, core domain superfamily / ATPase, nucleotide binding domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Alkaline phosphatase / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 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: 7JNG
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_ref_seq_dif / 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_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,0873
Polymers24,9912
Non-polymers961
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-21 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.710, 95.510, 117.220
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-803-

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: 1170.429 Da / Num. of mol.: 1 / Mutation: Q273R, F281S, A282R / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.6 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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.82→74.04 Å / Num. obs: 18615 / % possible obs: 96.3 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.05 / Rrim(I) all: 0.163 / Net I/σ(I): 8.4 / Num. measured all: 186551 / Scaling rejects: 651
Reflection shell

Diffraction-ID: 1 / Redundancy: 10.1 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.82-1.867.2121131111200.2182.3767.6110.598.2
9.11-74.040.05519461920.9990.0170.05827.398

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DKZ

1dkz


Resolution: 1.82→74.04 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.804 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2866 978 5.3 %RANDOM
Rwork0.2486 ---
obs0.2507 17631 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.29 Å2 / Biso mean: 36.988 Å2 / Biso min: 21.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å2-0 Å2
2--0.59 Å20 Å2
3----3.17 Å2
Refinement stepCycle: final / Resolution: 1.82→74.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 5 55 1685
Biso mean--100.64 41.93 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131643
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171547
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.6392220
X-RAY DIFFRACTIONr_angle_other_deg1.2561.5793603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50925.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66415299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.807156
X-RAY DIFFRACTIONr_chiral_restr0.0540.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
LS refinement shellResolution: 1.822→1.869 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 75 -
Rwork0.434 1305 -
all-1380 -
obs--97.53 %

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