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- PDB-6zbs: Beta ODAP Synthetase (BOS) -

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Basic information

Entry
Database: PDB / ID: 6zbs
TitleBeta ODAP Synthetase (BOS)
ComponentsBeta ODAP Synthetase (BOS)
KeywordsTRANSFERASE / Synthetase
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesLathyrus sativus (chickling vetch)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsDym, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2015839 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Identification and characterization of the key enzyme in the biosynthesis of the neurotoxin beta-ODAP in grass pea.
Authors: Goldsmith, M. / Barad, S. / Knafo, M. / Savidor, A. / Ben-Dor, S. / Brandis, A. / Mehlman, T. / Peleg, Y. / Albeck, S. / Dym, O. / Ben-Zeev, E. / Barbole, R.S. / Aharoni, A. / Reich, Z.
History
DepositionJun 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 4, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta ODAP Synthetase (BOS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6295
Polymers49,3691
Non-polymers2614
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-8 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.200, 66.200, 226.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

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Components

#1: Protein Beta ODAP Synthetase (BOS)


Mass: 49368.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lathyrus sativus (chickling vetch) / Production host: Escherichia coli K-12 (bacteria)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7 / Details: 0.1M MgCl2 0.05M HEPES pH=7 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→46.81 Å / Num. obs: 21933 / % possible obs: 98.83 % / Redundancy: 19.3 % / CC1/2: 0.75 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.165 / Net I/σ(I): 49.73
Reflection shellResolution: 2.35→2.434 Å / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 5.75 / Num. unique obs: 2130 / CC1/2: 0.824 / Rpim(I) all: 0.2717 / % possible all: 99.77

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KE4

4ke4


Resolution: 2.35→46.81 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1112 5.08 %
Rwork0.2061 20795 -
obs0.2089 21907 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.25 Å2 / Biso mean: 43.7092 Å2 / Biso min: 19.29 Å2
Refinement stepCycle: final / Resolution: 2.35→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 13 111 3452
Biso mean--47.75 40.3 -
Num. residues----424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.35-2.45690.33961420.25342533
2.4569-2.58650.28621240.24042532
2.5865-2.74850.27441250.23032565
2.7485-2.96070.33991300.23762553
2.9607-3.25860.28011350.22412575
3.2586-3.72990.26171360.20932606
3.7299-4.69860.23141560.17442627
4.6986-46.810.23211640.1932804

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