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- PDB-8bsa: Vc1313-LBD bound to D-arginine -

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Basic information

Entry
Database: PDB / ID: 8bsa
TitleVc1313-LBD bound to D-arginine
ComponentsMethyl-accepting chemotaxis protein
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-ARGININE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / 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
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)40,4794
Polymers40,1292
Non-polymers3502
Water2,576143
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2402
Polymers20,0641
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2402
Polymers20,0641
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.499, 44.557, 55.337
Angle α, β, γ (deg.)75.810, 84.490, 74.740
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


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-DAR / D-ARGININE


Type: D-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 0.1 M Tris (base) bicine pH 8.6 - 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-arginine from a 200 mM stock. ...Details: 0.1 M Tris (base) bicine pH 8.6 - 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-arginine 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: 8.6-8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.9→37.12 Å / Num. obs: 26099 / % possible obs: 96.32 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.43 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.0864 / Rpim(I) all: 0.0554 / Rrim(I) all: 0.1031 / Net I/σ(I): 7.46
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 2611 / CC1/2: 0.58 / CC star: 0.857

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.20rc3_4406refinement
Arcimboldophasing
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.9→37.12 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2245 --
Rwork0.1914 25126 -
obs-26087 96.32 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.95 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 24 143 2683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742578
X-RAY DIFFRACTIONf_angle_d0.95553494
X-RAY DIFFRACTIONf_chiral_restr0.0422401
X-RAY DIFFRACTIONf_plane_restr0.0084455
X-RAY DIFFRACTIONf_dihedral_angle_d4.9578347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-20.37411380.32463628X-RAY DIFFRACTION97.44
2-2.130.24651400.24893650X-RAY DIFFRACTION97.35
2.13-2.290.23361380.20323599X-RAY DIFFRACTION97.12
2.29-2.520.24671390.18183641X-RAY DIFFRACTION97.57
2.52-2.880.25311360.20193570X-RAY DIFFRACTION96.61
2.88-3.630.26691360.18983564X-RAY DIFFRACTION94.85
3.63-37.120.16651340.17033474X-RAY DIFFRACTION93.42
Refinement TLS params.Method: refined / Origin x: 5.81939976994 Å / Origin y: 17.0949914223 Å / Origin z: 35.8369548662 Å
111213212223313233
T0.268793693919 Å2-0.0159214337759 Å20.0133707848769 Å2-0.275200122998 Å2-0.0061910219882 Å2--0.326624542361 Å2
L1.10722647261 °2-0.113414038854 °20.351597134075 °2-0.729094820902 °2-0.123007063435 °2--0.774037105544 °2
S-0.0388180521425 Å °-0.0174251710999 Å °0.185604194384 Å °-0.151271332535 Å °-0.0223768657614 Å °-0.0125644191339 Å °-0.00643232137452 Å °0.0320803351927 Å °0.0726694011146 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1

IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1{A|32 - 476}AA - E32 - 4761
2{B|32 - 467}B32 - 467

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