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- PDB-8yke: Structure of two consecutively arrayed Rib domains (Rib8-9) from ... -

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Basic information

Entry
Database: PDB / ID: 8yke
TitleStructure of two consecutively arrayed Rib domains (Rib8-9) from surface adhesin of Limosilactobacillus reuteri
ComponentsYSIRK signal domain/LPXTG anchor domain surface protein
KeywordsSTRUCTURAL PROTEIN / cell surface protein / bacterial adhesin / rib domain / ig-like domain / tandem-repeat domain
Function / homology
Function and homology information


extracellular region / metal 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/alpha/Esp surface antigen / Rib domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...Putative pectate lyase-like adhesive domain / Putative pectate lyase-like adhesive domain / Long Rib domain / Long Rib domain / Rib/alpha/Esp surface antigen / Rib domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold
Similarity search - Domain/homology
YSIRK signal domain/LPXTG anchor domain surface protein
Similarity search - Component
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXue, Y. / Kang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22074070 China
CitationJournal: To Be Published
Title: Structure of two rib domains
Authors: Xue, Y. / Kang, X.
History
DepositionMar 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YSIRK signal domain/LPXTG anchor domain surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5592
Polymers16,4371
Non-polymers1221
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.085, 76.085, 51.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1859-

HOH

21A-1882-

HOH

31A-2065-

HOH

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Components

#1: Protein YSIRK signal domain/LPXTG anchor domain surface protein


Mass: 16436.646 Da / Num. of mol.: 1 / Fragment: two sequentially arrayed rib domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus reuteri (bacteria) / Gene: DB325_02015 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2T5Q5G6
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M NH4OAc, 0.1M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: May 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→24.1 Å / Num. obs: 14648 / % possible obs: 99.99 % / Redundancy: 43.1 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 25.4
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.631 / Num. unique obs: 2126 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
SAINTdata scaling
SADABSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→24.06 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 755 5.16 %
Rwork0.1637 --
obs0.1663 14627 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→24.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1153 0 8 291 1452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081225
X-RAY DIFFRACTIONf_angle_d0.9121700
X-RAY DIFFRACTIONf_dihedral_angle_d11.013451
X-RAY DIFFRACTIONf_chiral_restr0.055198
X-RAY DIFFRACTIONf_plane_restr0.007231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.24921480.18632696X-RAY DIFFRACTION100
1.94-2.130.25031430.16792727X-RAY DIFFRACTION100
2.13-2.440.23551380.17312755X-RAY DIFFRACTION100
2.44-3.080.21361570.16852778X-RAY DIFFRACTION100
3.08-24.060.17921690.14742916X-RAY DIFFRACTION100

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