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- PDB-9avk: Structure of long Rib domain from Limosilactobacillus reuteri -

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Basic information

Entry
Database: PDB / ID: 9avk
TitleStructure of long Rib domain from Limosilactobacillus reuteri
ComponentsYSIRK signal domain/LPXTG anchor domain surface protein
KeywordsSTRUCTURAL PROTEIN / cell surface protein / bacterial adhesin / rib domain / ig-like 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
THIOCYANATE ION / YSIRK signal domain/LPXTG anchor domain surface protein
Similarity search - Component
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.46 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 long Rib domain of the LPXTG-anchored surface protein from Limosilactobacillus reuteri.
Authors: Xue, Y. / Wu, Z. / Kang, X.
History
DepositionMar 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 12, 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

Downloads & links

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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)11,0433
Polymers10,9621
Non-polymers812
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-12 kcal/mol
Surface area6160 Å2
Unit cell
Length a, b, c (Å)36.161, 36.161, 126.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-1002-

SCN

21A-1002-

SCN

31A-1002-

SCN

41A-1101-

HOH

51A-1151-

HOH

61A-1193-

HOH

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Components

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


Mass: 10961.841 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 888-990
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.88 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.4 M Na Malonate pH 7, 0.2 M NaSCN

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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: Jul 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.46→23.8 Å / Num. obs: 14807 / % possible obs: 95.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.2
Reflection shellResolution: 1.46→1.56 Å / Rmerge(I) obs: 0.343 / Num. unique obs: 2036

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SADABSdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→23.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.941 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18257 734 5 %RANDOM
Rwork0.15388 ---
obs0.15536 14016 95.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.491 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.46→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms743 0 4 183 930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.011834
X-RAY DIFFRACTIONr_bond_other_d0.0010.016720
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.6931160
X-RAY DIFFRACTIONr_angle_other_deg0.5631.5531701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8455114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.63752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15410114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02965
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02139
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_it1.2940.857439
X-RAY DIFFRACTIONr_mcbond_other1.230.856438
X-RAY DIFFRACTIONr_mcangle_it2.0921.275558
X-RAY DIFFRACTIONr_mcangle_other2.0911.279559
X-RAY DIFFRACTIONr_scbond_it1.7110.995395
X-RAY DIFFRACTIONr_scbond_other1.6230.996395
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4521.417602
X-RAY DIFFRACTIONr_long_range_B_refined12.18827.7991058
X-RAY DIFFRACTIONr_long_range_B_other10.51919.704957
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.497 Å
RfactorNum. reflection% reflection
Rfree0.313 45 -
Rwork0.298 563 -
obs--54.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5655-0.07950.16080.3078-0.00880.18770-0.0197-0.0084-0.0070.0012-0.0212-0.0003-0.002-0.00120.00090.0009-0.00090.0265-0.00220.004716.1603-6.974210.9797
20.9779-0.32560.35140.361-0.12570.38020.0049-0.03270.0133-0.0254-0.0096-0.00360.0133-0.01490.00480.0118-0.00810.00380.0183-0.00910.005713.7883-5.98319.4586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A887 - 987
2X-RAY DIFFRACTION1A1001
3X-RAY DIFFRACTION2A1101 - 1283
4X-RAY DIFFRACTION2A1002

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