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- PDB-8yk7: Structure of Rib domain from surface adhesin of Limosilactobacill... -

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Basic information

Entry
Database: PDB / ID: 8yk7
TitleStructure of Rib domain 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
COPPER (II) ION / YSIRK signal domain/LPXTG anchor domain surface protein
Similarity search - Component
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsXue, Y. / Kang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22074070 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Crystal structure of the Rib domain of the cell-wall-anchored surface protein from Limosilactobacillus reuteri.
Authors: Xue, Y. / Wu, Z. / Kang, X.
History
DepositionMar 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)8,8016
Polymers8,5261
Non-polymers2745
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-16 kcal/mol
Surface area4840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.274, 76.274, 23.326
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 8526.283 Da / Num. of mol.: 1 / Fragment: Rib domain
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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.01M ZnSO4, 0.1M MES pH 6.5, 20% PEGMME 550, protein is premixed with 3mM CuCl2

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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: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.35→19.91 Å / Num. obs: 17478 / % possible obs: 99.7 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.2
Reflection shellResolution: 1.35→1.45 Å / Rmerge(I) obs: 0.4 / Num. unique obs: 3451

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SAINTdata scaling
SADABSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→19.91 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.747 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16725 851 4.9 %RANDOM
Rwork0.127 ---
obs0.12901 16600 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.356 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.35→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms595 0 11 126 732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.012647
X-RAY DIFFRACTIONr_bond_other_d0.0010.016574
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.688893
X-RAY DIFFRACTIONr_angle_other_deg0.4761.571359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.569587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.5841092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02728
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0296
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5790.93333
X-RAY DIFFRACTIONr_mcbond_other1.59635.888333
X-RAY DIFFRACTIONr_mcangle_it2.0651.41419
X-RAY DIFFRACTIONr_mcangle_other2.0731.663420
X-RAY DIFFRACTIONr_scbond_it2.8141.168314
X-RAY DIFFRACTIONr_scbond_other3.1315
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0881.662473
X-RAY DIFFRACTIONr_long_range_B_refined4.061804
X-RAY DIFFRACTIONr_long_range_B_other3.181739
X-RAY DIFFRACTIONr_rigid_bond_restr2.7333647
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.382 Å
RfactorNum. reflection% reflection
Rfree0.224 66 -
Rwork0.227 1219 -
obs--99.54 %
Refinement TLS params.Method: refined / Origin x: -5.545 Å / Origin y: 30.229 Å / Origin z: -2.459 Å
111213212223313233
T0.0127 Å2-0.005 Å2-0.005 Å2-0.028 Å20.0025 Å2--0.0103 Å2
L1.0265 °20.4389 °2-0.5157 °2-0.282 °2-0.267 °2--0.5288 °2
S0.0243 Å °0.0381 Å °0.0162 Å °0.0251 Å °-0.0273 Å °-0.0118 Å °0.0259 Å °-0.0124 Å °0.003 Å °

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