[English] 日本語
Yorodumi
- PDB-7rfq: STRUCTURE OF BACTERIAL SYLF DOMAIN CONTAINING PROTEIN, BETA CELL ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rfq
TitleSTRUCTURE OF BACTERIAL SYLF DOMAIN CONTAINING PROTEIN, BETA CELL EXPANSION FACTOR A (BEFA)
ComponentsBETA CELL EXPANSION FACTOR A (BEFA)
KeywordsSIGNALING PROTEIN / SYLF DOMAIN / BACTERIAL PROTEIN / DEVELOPMENTAL REGULATOR / BETA CELL EXPANSION FACTOR
Function / homologyhost cellular component / extracellular region / CITRIC ACID / Beta cell expansion factor A
Function and homology information
Biological speciesAeromonas veronii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.27 Å
AuthorsSweeney, E.G.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)
Citation
Journal: Cell Metab. / Year: 2022
Title: BefA, a microbiota-secreted membrane disrupter, disseminates to the pancreas and increases beta cell mass.
Authors: Hill, J.H. / Massaquoi, M.S. / Sweeney, E.G. / Wall, E.S. / Jahl, P. / Bell, R. / Kallio, K. / Derrick, D. / Murtaugh, L.C. / Parthasarathy, R. / Remington, S.J. / Round, J.L. / Guillemin, K.
#1: Journal: Elife / Year: 2016
Title: A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development.
Authors: Hill, J.H. / Franzosa, E.A. / Huttenhower, C. / Guillemin, K.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA CELL EXPANSION FACTOR A (BEFA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2233
Polymers29,8391
Non-polymers3842
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.670, 64.550, 42.630
Angle α, β, γ (deg.)90.000, 113.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-602-

HOH

31A-609-

HOH

-
Components

#1: Protein BETA CELL EXPANSION FACTOR A (BEFA)


Mass: 29838.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas veronii (bacteria) / Gene: AMS64_07270 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S3XLU2
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.01 Å3/Da / Density % sol: 38.66 % / Description: diamond-like, embedded in sticky precipitant
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 25 % PEG 3350, 100 mM CITRIC ACID PH 3.5, 1 mM TCEP, 39 mM O-PHOSPHO-L-SERINE OR 39 mM SERINE, VAPOR

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0, 0.9795
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
ReflectionResolution: 1.27→37.35 Å / Num. all: 62064 / Num. obs: 62064 / % possible obs: 100 % / Redundancy: 10 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.177 / Rsym value: 0.168 / Net I/av σ(I): 2.4 / Net I/σ(I): 8.7 / Num. measured all: 621902
Reflection shellResolution: 1.27→1.32 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 5 / Num. measured all: 23389 / Num. unique obs: 2032 / Rpim(I) all: 0.035 / Rrim(I) all: 0.119 / Rsym value: 0.114 / Net I/σ(I) obs: 17.2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.27→37.35 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.54
RfactorNum. reflection% reflection
Rfree0.155 2308 3.72 %
Rwork0.131 59730 -
obs0.132 62038 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.51 Å2 / Biso mean: 18.8979 Å2 / Biso min: 5.01 Å2
Refinement stepCycle: final / Resolution: 1.27→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 36 222 1951
Biso mean--42.47 37.42 -
Num. residues----223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.27-1.29760.2381370.1918369099
1.2976-1.32780.19051580.15943680100
1.3278-1.3610.16921330.14083767100
1.361-1.39780.16611550.13163681100
1.3978-1.4390.16741430.12633716100
1.439-1.48540.141430.12123738100
1.4854-1.53850.14611470.10643702100
1.5385-1.60010.12891430.10623757100
1.6001-1.67290.15771320.1113709100
1.6729-1.76110.13231440.11193720100
1.7611-1.87140.16191470.11593742100
1.8714-2.01590.13451450.11443742100
2.0159-2.21880.13621380.11723755100
2.2188-2.53980.15191530.12623730100
2.5398-3.19960.14971480.14373776100
3.1996-37.30.1711420.14843825100

+
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