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- PDB-6mni: Structure of the tandem CACHE domain of PscC -

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Basic information

Entry
Database: PDB / ID: 6mni
TitleStructure of the tandem CACHE domain of PscC
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / tandem CACHE domain / chemoreceptor / ligand complex / Pseudomonas syringae pv. actinidiae / PscC
Function / homology
Function and homology information


transmembrane signaling receptor activity / chemotaxis / membrane => GO:0016020 / signal transduction / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain ...Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
PROLINE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesPseudomonas syringae pv. actinidiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 Å
AuthorsJohnston, J.M. / Gerth, M.L. / Ehrhardt, M.K.G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structure of a double CACHE chemoreceptor ligand-binding domain from Pseudomonas syringae provides insights into the basis of proline recognition.
Authors: Ehrhardt, M.K.G. / Gerth, M.L. / Johnston, J.M.
History
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5976
Polymers63,2392
Non-polymers3584
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-23 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.244, 53.916, 73.312
Angle α, β, γ (deg.)104.790, 91.200, 92.710
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Methyl-accepting chemotaxis protein


Mass: 31619.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: this protein is a N-terminal His-tag construct of the tandem CACHE domain of the full length protein PscC. The numbering in the PDB file is such that the residues match the numbering of the ...Details: this protein is a N-terminal His-tag construct of the tandem CACHE domain of the full length protein PscC. The numbering in the PDB file is such that the residues match the numbering of the full length protein. The tag from the construct is not visualised in the structure.
Source: (gene. exp.) Pseudomonas syringae pv. actinidiae (bacteria)
Gene: KPSA3_03559 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V0QX35
#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-tris pH 5.5 and 30% PEG3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953724086285 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724086285 Å / Relative weight: 1
ReflectionResolution: 1.696→48.272 Å / Num. obs: 54175 / % possible obs: 96.6 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.047 / Rrim(I) all: 0.089 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.733.40.4631.426620.8160.2880.54789.2
8.98-48.273.60.0543620.9940.0330.06397.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c8c

3c8c


Resolution: 1.696→48.272 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 20.42
RfactorNum. reflection% reflection
Rfree0.1999 2577 4.76 %
Rwork0.1622 --
obs0.1641 54162 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.49 Å2 / Biso mean: 28.1792 Å2 / Biso min: 11.04 Å2
Refinement stepCycle: final / Resolution: 1.696→48.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 23 382 4295
Biso mean--23.87 36.07 -
Num. residues----509
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6963-1.72890.2841310.25562667279890
1.7289-1.76420.24831490.20142796294596
1.7642-1.80260.22611480.18612914306296
1.8026-1.84450.22921530.17662801295497
1.8445-1.89060.22681210.17142899302097
1.8906-1.94180.191430.17112857300096
1.9418-1.99890.21611570.172874303197
1.9989-2.06340.21571190.16272884300397
2.0634-2.13720.20551340.1632914304897
2.1372-2.22270.2291280.16152868299697
2.2227-2.32390.21381250.16582925305097
2.3239-2.44640.22391410.1712912305398
2.4464-2.59970.2061450.16752905305098
2.5997-2.80040.20711440.17652880302498
2.8004-3.08220.21381540.16452918307298
3.0822-3.5280.20111760.15732810298697
3.528-4.44450.16041560.13922863301996
4.4445-48.29120.18031530.15352898305198

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