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- PDB-7rfq: STRUCTURE OF BACTERIAL SYLF DOMAIN CONTAINING PROTEIN, BETA CELL ... -

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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 / homologyCITRIC ACID / Uncharacterized protein
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.01 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

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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

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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

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