[English] 日本語
Yorodumi
- PDB-6s5w: Structure of Rib domain 'Rib Long' from Lactobacillus acidophilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s5w
TitleStructure of Rib domain 'Rib Long' from Lactobacillus acidophilus
ComponentsSurface protein
KeywordsSTRUCTURAL PROTEIN / Rib domain / bacterial cell surface / immunoglobulin fold / profile-HMM / domain atrophy
Function / homology
Function and homology information


calcium 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 / Cadherin-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsGriffiths, S.C. / Cooper, R.E.M. / Whelan, F. / Whittingham, J.L. / Bateman, A. / Potts, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart Foundation United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection.
Authors: Whelan, F. / Lafita, A. / Griffiths, S.C. / Cooper, R.E.M. / Whittingham, J.L. / Turkenburg, J.P. / Manfield, I.W. / St John, A.N. / Paci, E. / Bateman, A. / Potts, J.R.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: 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 1.2Dec 21, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Surface protein
B: Surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0366
Polymers22,7242
Non-polymers3114
Water6,864381
1
A: Surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6504
Polymers11,3621
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3852
Polymers11,3621
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.370, 147.810, 56.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1458-

HOH

21A-1516-

HOH

31A-1527-

HOH

41A-1546-

HOH

51A-1560-

HOH

61A-1561-

HOH

71B-1485-

HOH

81B-1573-

HOH

-
Components

#1: Protein Surface protein


Mass: 11362.205 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: LBA1633 / Plasmid: pETFPP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5FIM8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium Sulphate, 30% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.07→44.95 Å / Num. obs: 78337 / % possible obs: 97.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 10.016 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Net I/σ(I): 13.2
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3096 / CC1/2: 0.312

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
ACORNphasing
ARP/wARPmodel building
Fragonphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→44.946 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.9
RfactorNum. reflection% reflection
Rfree0.1777 3779 4.83 %
Rwork0.1472 --
obs0.1487 78305 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.07→44.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 16 381 1958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061708
X-RAY DIFFRACTIONf_angle_d0.8812372
X-RAY DIFFRACTIONf_dihedral_angle_d13.407644
X-RAY DIFFRACTIONf_chiral_restr0.079267
X-RAY DIFFRACTIONf_plane_restr0.008330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.08350.33611110.29322148X-RAY DIFFRACTION76
1.0835-1.09780.331100.282390X-RAY DIFFRACTION85
1.0978-1.11280.29741290.24742598X-RAY DIFFRACTION91
1.1128-1.12870.25571270.23932600X-RAY DIFFRACTION94
1.1287-1.14560.2461450.22182668X-RAY DIFFRACTION95
1.1456-1.16350.24941280.21332739X-RAY DIFFRACTION96
1.1635-1.18260.20211370.20442744X-RAY DIFFRACTION98
1.1826-1.2030.22641350.19182754X-RAY DIFFRACTION97
1.203-1.22480.17111340.17662765X-RAY DIFFRACTION99
1.2248-1.24840.17081350.15992764X-RAY DIFFRACTION98
1.2484-1.27390.19391440.15442797X-RAY DIFFRACTION99
1.2739-1.30160.1751370.14072800X-RAY DIFFRACTION100
1.3016-1.33190.18121290.14332807X-RAY DIFFRACTION99
1.3319-1.36520.17291320.13692813X-RAY DIFFRACTION99
1.3652-1.40210.18511400.14372830X-RAY DIFFRACTION100
1.4021-1.44330.1741540.14242817X-RAY DIFFRACTION100
1.4433-1.48990.19331580.13832810X-RAY DIFFRACTION100
1.4899-1.54320.18321490.12932825X-RAY DIFFRACTION100
1.5432-1.6050.1531410.13062833X-RAY DIFFRACTION100
1.605-1.6780.16821710.12992811X-RAY DIFFRACTION100
1.678-1.76650.15751610.1332822X-RAY DIFFRACTION100
1.7665-1.87720.15461250.13412871X-RAY DIFFRACTION100
1.8772-2.02210.14811670.12872831X-RAY DIFFRACTION100
2.0221-2.22560.15081420.1272874X-RAY DIFFRACTION100
2.2256-2.54760.17921460.14222888X-RAY DIFFRACTION100
2.5476-3.20960.17821440.14682912X-RAY DIFFRACTION100
3.2096-44.98560.1791480.14653015X-RAY DIFFRACTION99

+
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://pdbjlvh1.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