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- PDB-5ny0: L. reuters 100-23 SRRP -

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Basic information

Entry
Database: PDB / ID: 5ny0
TitleL. reuters 100-23 SRRP
ComponentsL. reuteris SRRP binding region
KeywordsCELL ADHESION / beta-solenoid / L. reuteri / adhesin
Function / homologyPutative pectate lyase-like adhesive domain / Putative pectate lyase-like adhesive domain / L. reuteris SRRP binding region
Function and homology information
Biological speciesLactobacillus reuteri 100-23 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSequeira, S. / Dong, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust 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 11, 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 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: L. reuteris SRRP binding region


Theoretical massNumber of molelcules
Total (without water)39,4401
Polymers39,4401
Non-polymers00
Water3,603200
1
A: L. reuteris SRRP binding region

A: L. reuteris SRRP binding region


Theoretical massNumber of molelcules
Total (without water)78,8802
Polymers78,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area1740 Å2
ΔGint-5 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.356, 162.356, 146.777
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-829-

HOH

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Components

#1: Protein L. reuteris SRRP binding region


Mass: 39439.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri 100-23 (bacteria)
Gene: srrp / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: A0A384E0N5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 4.74 Å3/Da / Density % sol: 74.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.2 M sodium tartrate dibasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 2.2→65.06 Å / Num. obs: 37741 / % possible obs: 100 % / Redundancy: 9.2 % / Net I/σ(I): 21.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 5 / Num. unique obs: 5451 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NXK

5nxk


Resolution: 2→49.969 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 2507 5.01 %RANDOM
Rwork0.2241 ---
obs0.2251 50049 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→49.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 0 200 2786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132629
X-RAY DIFFRACTIONf_angle_d1.3973582
X-RAY DIFFRACTIONf_dihedral_angle_d12.23909
X-RAY DIFFRACTIONf_chiral_restr0.064422
X-RAY DIFFRACTIONf_plane_restr0.006467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03850.25451360.21332600X-RAY DIFFRACTION100
2.0385-2.08010.24691440.21032621X-RAY DIFFRACTION100
2.0801-2.12530.2351190.21892647X-RAY DIFFRACTION100
2.1253-2.17480.26381350.22812602X-RAY DIFFRACTION100
2.1748-2.22920.26481510.22722606X-RAY DIFFRACTION100
2.2292-2.28940.26741450.24072624X-RAY DIFFRACTION100
2.2894-2.35680.28641480.23152621X-RAY DIFFRACTION100
2.3568-2.43290.29871320.22792633X-RAY DIFFRACTION100
2.4329-2.51980.22921390.23052655X-RAY DIFFRACTION100
2.5198-2.62070.26841420.22522622X-RAY DIFFRACTION100
2.6207-2.740.26381310.23392618X-RAY DIFFRACTION100
2.74-2.88440.26571180.23412666X-RAY DIFFRACTION100
2.8844-3.06510.24721410.23432646X-RAY DIFFRACTION100
3.0651-3.30170.25591550.2372629X-RAY DIFFRACTION100
3.3017-3.63390.24511400.21862659X-RAY DIFFRACTION100
3.6339-4.15950.22451580.22032652X-RAY DIFFRACTION100
4.1595-5.23960.21081390.20652686X-RAY DIFFRACTION100
5.2396-49.98460.26141340.23062755X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -2.4156 Å / Origin y: 27.5352 Å / Origin z: 50.4817 Å
111213212223313233
T0.3366 Å2-0.0626 Å20.0317 Å2-0.343 Å20.0105 Å2--0.3359 Å2
L0.4578 °2-0.2524 °20.3777 °2-0.7271 °2-0.1341 °2--0.7584 °2
S-0.0163 Å °0.1023 Å °-0.0595 Å °-0.1232 Å °0.0769 Å °0.0415 Å °0.0488 Å °0.0663 Å °-0.001 Å °
Refinement TLS groupSelection details: all

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