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- PDB-6sx1: Structure of Rib Standard, a Rib domain from Lactobacillus acidophilus -

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Basic information

Entry
Database: PDB / ID: 6sx1
TitleStructure of Rib Standard, a Rib domain from Lactobacillus acidophilus
ComponentsSurface proteinCell membrane
KeywordsSTRUCTURAL PROTEIN / Rib domain / bacterial cell surface / immunoglobulin fold / profile-HMM / domain atrophy
Function / homology
Function and homology information


calcium ion binding / membrane
Similarity search - Function
Putative pectate lyase-like adhesive domain / Putative pectate lyase-like adhesive domain / Long Rib domain / Long Rib domain / Rib domain / Rib/alpha/Esp surface antigen / Cadherin-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsCooper, R.E.M. / Griffiths, S.C. / Turkenburg, J.P. / Bateman, A. / Potts, J.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
British Heart Foundation United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection.
Authors: Whelan, F. / Lafita, A. / Griffiths, S.C. / Cooper, R.E.M. / Whittingham, J.L. / Turkenburg, J.P. / Manfield, I.W. / St John, A.N. / Paci, E. / Bateman, A. / Potts, J.R.
History
DepositionSep 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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: Surface protein


Theoretical massNumber of molelcules
Total (without water)8,7281
Polymers8,7281
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Rib Short is a monomer in solution as verified by SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.183, 32.644, 62.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Surface protein / Cell membrane


Mass: 8728.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Rib Standard (residues 1269-1351) from Lactobacillus acidophilus, recombinantly overexpressed and purified using the pET_FPP1 vector in Escherichia coli
Source: (gene. exp.) Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM) (bacteria)
Strain: ATCC 700396 / NCK56 / N2 / NCFM / Gene: LBA1633 / Plasmid: pET_FPP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / References: UniProt: Q5FIM8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.77 Å3/Da / Density % sol: 30.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2M ammonium sulphate, 2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.25→31.42 Å / Num. obs: 17774 / % possible obs: 99.8 % / Redundancy: 1.9 % / CC1/2: 1 / Net I/σ(I): 16.6
Reflection shellResolution: 1.25→1.27 Å / Num. unique obs: 773 / CC1/2: 0.961 / % possible all: 90.4

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Processing

Software
NameClassification
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→31.42 Å / Cross valid method: THROUGHOUT /
Num. reflection% reflection
obs17665 99.3 %
Refinement stepCycle: LAST / Resolution: 1.25→31.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms585 0 0 75 660

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