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- PDB-8bsb: Vc1313-LBD bound to D-lysine -

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Basic information

Entry
Database: PDB / ID: 8bsb
TitleVc1313-LBD bound to D-lysine
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsMEMBRANE PROTEIN / ligand binding domain / Methyl-accepting chemotaxis protein / chemotaxis
Function / homology
Function and homology information


chemotaxis / signal transduction / membrane
Similarity search - Function
Chemotaxis methyl-accepting receptor HlyB-like, 4HB MCP domain / Four helix bundle sensory module for signal transduction / 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
D-LYSINE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Authorster Beek, J. / Berntsson, R.P.-A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-03599 Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Microbiol / Year: 2023
Title: D-amino acids signal a stress-dependent run-away response in Vibrio cholerae.
Authors: Irazoki, O. / Ter Beek, J. / Alvarez, L. / Mateus, A. / Colin, R. / Typas, A. / Savitski, M.M. / Sourjik, V. / Berntsson, R.P. / Cava, F.
History
DepositionNov 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 15, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.5May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)40,4214
Polymers40,1292
Non-polymers2922
Water2,396133
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2112
Polymers20,0641
Non-polymers1461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2112
Polymers20,0641
Non-polymers1461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.337, 44.927, 56.939
Angle α, β, γ (deg.)75.320, 79.170, 73.690
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins


Mass: 20064.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: FLM12_13895 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B3LML0
#2: Chemical ChemComp-DLY / D-LYSINE / Lysine


Type: D-peptide linking / Mass: 146.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 0.1 M Tris (base) bicine pH 8.2 - 8.8, 17 - 21% v/v PEG 500 MME, 8 - 10% w/v PEG 20000. Before setting up the drops 13 mg ml-1 Vc1313-LBD was mixed with 10 mM D-lysine from a 200 mM stock. ...Details: 0.1 M Tris (base) bicine pH 8.2 - 8.8, 17 - 21% v/v PEG 500 MME, 8 - 10% w/v PEG 20000. Before setting up the drops 13 mg ml-1 Vc1313-LBD was mixed with 10 mM D-lysine from a 200 mM stock. The protein-ligand mixture was then mixed with reservoir solution in a 3:1 ratio. Before flash freezing the crystal in liquid nitrogen, the PEG concentrations were raised to 23% v/v PEG 500*MME, 12% w/v PEG 20000.
PH range: 8.2-8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→36.5 Å / Num. obs: 26736 / % possible obs: 96.88 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.63 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09516 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 0.8823 / Num. unique obs: 2676 / CC1/2: 0.612

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
REFMAC5refinement
PHENIX1.20rc3_4406phasing
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Vc1313-LBD with D-arg

Resolution: 1.9→36.5 Å / SU ML: 0.2529 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.4671
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2328 667 2.5 %
Rwork0.1885 26061 -
obs0.1895 26728 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.91 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 20 133 2696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322620
X-RAY DIFFRACTIONf_angle_d0.5323553
X-RAY DIFFRACTIONf_chiral_restr0.0327408
X-RAY DIFFRACTIONf_plane_restr0.0038462
X-RAY DIFFRACTIONf_dihedral_angle_d4.6216355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.050.34981320.31255182X-RAY DIFFRACTION96.69
2.05-2.250.30381340.22915236X-RAY DIFFRACTION96.55
2.25-2.580.2461340.18845216X-RAY DIFFRACTION97.5
2.58-3.250.26161340.18165263X-RAY DIFFRACTION97.61
3.25-36.50.18541330.16645164X-RAY DIFFRACTION96.15
Refinement TLS params.Method: refined / Origin x: -5.66655293793 Å / Origin y: 5.32114121963 Å / Origin z: -19.3925904294 Å
111213212223313233
T0.216918454954 Å2-0.0120359298487 Å20.0363276521936 Å2-0.240827273762 Å2-0.000763585121022 Å2--0.24033286291 Å2
L0.556967514045 °20.0375337941152 °20.0463504098496 °2-0.65646305871 °2-0.107024394774 °2--0.326990929594 °2
S0.000477822413851 Å °-0.000222976074378 Å °0.0480565122745 Å °-0.0845997515465 Å °-0.00328332916111 Å °0.0116074538595 Å °0.0152721359645 Å °-0.0175304127471 Å °0.00602496626966 Å °
Refinement TLS groupSelection details: all

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