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- PDB-5nxk: L. reuteri 53608 SRRP -

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Basic information

Entry
Database: PDB / ID: 5nxk
TitleL. reuteri 53608 SRRP
ComponentsSerine-rich secreted cell wall anchored (LPXTG-motif ) protein
KeywordsCELL ADHESION / beta-solenoid / L. reuteri / adhesin
Function / homology:
Function and homology information
Biological speciesLactobacillus reuteri ATCC 53608 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.918 Å
AuthorsSequeira, S. / Dong, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT106121 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for the role of serine-rich repeat proteins from Lactobacillus reuteriin gut microbe-host interactions.
Authors: Sequeira, S. / Kavanaugh, D. / MacKenzie, D.A. / Suligoj, T. / Walpole, S. / Leclaire, C. / Gunning, A.P. / Latousakis, D. / Willats, W.G.T. / Angulo, J. / Dong, C. / Juge, N.
History
DepositionMay 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine-rich secreted cell wall anchored (LPXTG-motif ) protein
B: Serine-rich secreted cell wall anchored (LPXTG-motif ) protein
C: Serine-rich secreted cell wall anchored (LPXTG-motif ) protein


Theoretical massNumber of molelcules
Total (without water)98,9663
Polymers98,9663
Non-polymers00
Water17,997999
1
A: Serine-rich secreted cell wall anchored (LPXTG-motif ) protein


Theoretical massNumber of molelcules
Total (without water)32,9891
Polymers32,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine-rich secreted cell wall anchored (LPXTG-motif ) protein


Theoretical massNumber of molelcules
Total (without water)32,9891
Polymers32,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine-rich secreted cell wall anchored (LPXTG-motif ) protein


Theoretical massNumber of molelcules
Total (without water)32,9891
Polymers32,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.697, 146.697, 110.423
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-712-

HOH

21A-837-

HOH

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Components

#1: Protein Serine-rich secreted cell wall anchored (LPXTG-motif ) protein


Mass: 32988.570 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri ATCC 53608 (bacteria)
Gene: LRATCC53608_0906 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0A0S4NNC0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 3.47 Å3/Da / Density % sol: 64.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M sodium malonate, 12% w/v PEG3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.92→73.35 Å / Num. obs: 104897 / % possible obs: 100 % / Redundancy: 18 % / Net I/σ(I): 9.9
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 15 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5168 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.918→19.77 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1825 5260 5.02 %RANDOM
Rwork0.157 ---
obs0.1583 104681 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.918→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6897 0 0 999 7896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086970
X-RAY DIFFRACTIONf_angle_d1.2369474
X-RAY DIFFRACTIONf_dihedral_angle_d12.0812488
X-RAY DIFFRACTIONf_chiral_restr0.0541155
X-RAY DIFFRACTIONf_plane_restr0.0051240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.918-1.93980.27551630.26513323X-RAY DIFFRACTION100
1.9398-1.96260.26751860.24193263X-RAY DIFFRACTION100
1.9626-1.98650.2621740.23223277X-RAY DIFFRACTION100
1.9865-2.01160.25271630.2283312X-RAY DIFFRACTION100
2.0116-2.03810.24541750.21733308X-RAY DIFFRACTION100
2.0381-2.06590.24691820.21833246X-RAY DIFFRACTION100
2.0659-2.09540.26441670.21173288X-RAY DIFFRACTION100
2.0954-2.12670.24121980.20793286X-RAY DIFFRACTION100
2.1267-2.15990.23521650.19643322X-RAY DIFFRACTION100
2.1599-2.19520.2151850.18073244X-RAY DIFFRACTION100
2.1952-2.2330.18391720.17253296X-RAY DIFFRACTION100
2.233-2.27360.22111580.18593289X-RAY DIFFRACTION100
2.2736-2.31720.21491790.16993307X-RAY DIFFRACTION100
2.3172-2.36450.21351730.16763296X-RAY DIFFRACTION100
2.3645-2.41580.19531820.16263315X-RAY DIFFRACTION100
2.4158-2.47190.21191740.1653277X-RAY DIFFRACTION100
2.4719-2.53360.18521960.1563283X-RAY DIFFRACTION100
2.5336-2.60190.1851570.15173323X-RAY DIFFRACTION100
2.6019-2.67830.18271910.15693305X-RAY DIFFRACTION100
2.6783-2.76450.1921610.15683334X-RAY DIFFRACTION100
2.7645-2.86310.19131580.15453307X-RAY DIFFRACTION100
2.8631-2.97730.17221940.14913303X-RAY DIFFRACTION100
2.9773-3.11240.15961680.14573354X-RAY DIFFRACTION100
3.1124-3.27570.17761710.14873307X-RAY DIFFRACTION100
3.2757-3.47990.17771650.13643345X-RAY DIFFRACTION100
3.4799-3.7470.14981890.12863341X-RAY DIFFRACTION100
3.747-4.12090.14591660.13053347X-RAY DIFFRACTION100
4.1209-4.71020.14631790.1163352X-RAY DIFFRACTION100
4.7102-5.9080.1481660.14413399X-RAY DIFFRACTION100
5.908-19.77090.17472030.16723472X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 69.0294 Å / Origin y: 18.8141 Å / Origin z: -6.4054 Å
111213212223313233
T0.171 Å2-0.0155 Å2-0.0104 Å2-0.0986 Å20.0045 Å2--0.1235 Å2
L0.1879 °20.0603 °20.0161 °2-0.2933 °20.1005 °2--0.1769 °2
S-0.0441 Å °-0.0222 Å °-0.0162 Å °-0.0815 Å °-0.0132 Å °0.0124 Å °-0.0323 Å °0.0158 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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