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- PDB-6dsp: LsrB from Clostridium saccharobutylicum in complex with AI-2 -

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Basic information

Entry
Database: PDB / ID: 6dsp
TitleLsrB from Clostridium saccharobutylicum in complex with AI-2
ComponentsAutoinducer 2-binding protein LsrB
KeywordsSIGNALING PROTEIN / AI-2 receptor
Function / homology
Function and homology information


: / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PAV / Autoinducer 2-binding protein LsrB
Similarity search - Component
Biological speciesClostridium saccharobutylicum DSM 13864 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsTorcato, I.M. / Xavier, K.B. / Miller, S.T.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Other governmentPTDC/BIA-MIC/4188/14 Portugal
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Identification of novel autoinducer-2 receptors inClostridiareveals plasticity in the binding site of the LsrB receptor family.
Authors: Torcato, I.M. / Kasal, M.R. / Brito, P.H. / Miller, S.T. / Xavier, K.B.
History
DepositionJun 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Aug 21, 2019Group: Data collection / 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
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 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: Autoinducer 2-binding protein LsrB
B: Autoinducer 2-binding protein LsrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0654
Polymers74,7642
Non-polymers3002
Water6,467359
1
A: Autoinducer 2-binding protein LsrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5322
Polymers37,3821
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Autoinducer 2-binding protein LsrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5322
Polymers37,3821
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.780, 90.780, 182.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11B-612-

HOH

21B-651-

HOH

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Components

#1: Protein Autoinducer 2-binding protein LsrB


Mass: 37382.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium saccharobutylicum DSM 13864 (bacteria)
Gene: lsrB, CLSA_c21430 / Plasmid: pDEST-527 / Production host: Escherichia coli (E. coli) / References: UniProt: U5MRH9
#2: Sugar ChemComp-PAV / (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Citric acid pH 2.75 and 26% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 1.37→50.49 Å / Num. obs: 160886 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Χ2: 0.79 / Net I/σ(I): 14.4
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7881 / CC1/2: 0.731 / Rpim(I) all: 0.509 / Rrim(I) all: 0.967 / Χ2: 0.61 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tjy

1tjy


Resolution: 1.37→50.49 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1772 2015 5 %
Rwork0.1592 --
obs-151878 99.95 %
Displacement parametersBiso mean: 19.77 Å2
Refinement stepCycle: LAST / Resolution: 1.37→50.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4948 0 20 359 5327
LS refinement shellResolution: 1.37→1.49 Å
RfactorNum. reflection% reflection
Rfree0.227 -5 %
Rwork0.2058 13527 -
obs--99.99 %

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