[English] 日本語
Yorodumi
- PDB-4ng0: Lar_0958 a cell surface adhesin from lactobacillus reuteri -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ng0
TitleLar_0958 a cell surface adhesin from lactobacillus reuteri
ComponentsLAR_0958 cell surface adhesin
KeywordsCELL ADHESION / ubiquitin-like beta-grasp fold / adhesin / mucus / cell surface
Function / homologyRibosomal Protein L9; domain 2 - #110 / Ribosomal Protein L9; domain 2 / Roll / Alpha Beta / :
Function and homology information
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.501 Å
AuthorsEtzold, S. / Mackenzie, D.A. / Juge, N. / Hemmings, A.M.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structural and molecular insights into novel surface-exposed mucus adhesins from Lactobacillus reuteri human strains.
Authors: Etzold, S. / MacKenzie, D.A. / Jeffers, F. / Walshaw, J. / Roos, S. / Hemmings, A.M. / Juge, N.
History
DepositionNov 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LAR_0958 cell surface adhesin
B: LAR_0958 cell surface adhesin
C: LAR_0958 cell surface adhesin


Theoretical massNumber of molelcules
Total (without water)31,3363
Polymers31,3363
Non-polymers00
Water12,430690
1
A: LAR_0958 cell surface adhesin


Theoretical massNumber of molelcules
Total (without water)10,4451
Polymers10,4451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LAR_0958 cell surface adhesin


Theoretical massNumber of molelcules
Total (without water)10,4451
Polymers10,4451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LAR_0958 cell surface adhesin


Theoretical massNumber of molelcules
Total (without water)10,4451
Polymers10,4451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.790, 36.990, 75.550
Angle α, β, γ (deg.)90.000, 100.640, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein LAR_0958 cell surface adhesin


Mass: 10445.415 Da / Num. of mol.: 3 / Fragment: Single repeat (UNP residues 577-672)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: JCM 1112 / Gene: B2G7P2_LACRJ, LAR_0958 / Plasmid: pETBlue-1 AccepTor / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER(DE3)pLacI / References: UniProt: B2G7P2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M Ammonium sulfate, 0.1M sodium acetate, 25% (w/v) PEG 4000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorDetector: AREA DETECTOR / Date: Dec 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.501→46.777 Å / Num. all: 45978 / Num. obs: 45978 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 11.67 Å2 / Rsym value: 0.028 / Net I/σ(I): 30.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.543.90.1425.51307333270.14297.8
1.54-1.584.10.1236.41328532750.12399.8
1.58-1.634.10.1027.71302131950.10299.8
1.63-1.684.10.0839.41295931830.08399.9
1.68-1.734.10.06911.21221729850.06999.9
1.73-1.794.10.0612.91200429330.0699.8
1.79-1.864.10.04815.81170828540.04899.9
1.86-1.944.10.03918.91125127380.03999.9
1.94-2.024.10.03321.61071725990.03399.9
2.02-2.124.10.02824.91028525070.028100
2.12-2.244.10.02725.4988823980.02799.9
2.24-2.374.10.02625.7926422610.026100
2.37-2.5440.02525.8860221440.02599.8
2.54-2.743.80.02325.6753019680.023100
2.74-33.70.02129.9687118370.02199.9
3-3.363.80.02127.9647016820.02199.8
3.36-3.873.80.01931.6548914330.01998.7
3.87-4.753.90.01640.7488512380.01697.7
4.75-6.713.90.01739.636819490.01796.8
6.71-46.7773.30.01740.415624720.01781.4

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.501→29.014 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8901 / SU ML: 0.12 / σ(F): 1.34 / Phase error: 17.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1872 2316 5.04 %RANDOM
Rwork0.1577 ---
obs0.1592 45963 99.3 %-
all-45963 --
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.3 Å2 / Biso mean: 15.9484 Å2 / Biso min: 3.07 Å2
Refinement stepCycle: LAST / Resolution: 1.501→29.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 0 690 2876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062284
X-RAY DIFFRACTIONf_angle_d0.9883141
X-RAY DIFFRACTIONf_chiral_restr0.066363
X-RAY DIFFRACTIONf_plane_restr0.004402
X-RAY DIFFRACTIONf_dihedral_angle_d8.971823
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5005-1.55420.23852540.18544256451098
1.5542-1.61640.24022330.174843574590100
1.6164-1.68990.22262130.165343684581100
1.6899-1.7790.19752020.166943574559100
1.779-1.89050.19672390.168343854624100
1.8905-2.03640.19052340.161343794613100
2.0364-2.24120.17572470.154643384585100
2.2412-2.56540.17572580.162343794637100
2.5654-3.23140.18782300.153644434673100
3.2314-29.01980.16592060.14374385459196

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more