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- PDB-6vl0: Crystal Structure of the N-prenyltransferase DabA in Complex with... -

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Basic information

Entry
Database: PDB / ID: 6vl0
TitleCrystal Structure of the N-prenyltransferase DabA in Complex with GSPP and Mn2+
ComponentsDabA
KeywordsTRANSFERASE / prenyltransferase / terpene cyclase
Function / homology
Function and homology information


cellular response to carbon dioxide / Transferases; Transferring alkyl or aryl groups, other than methyl groups / cellular response to phosphate starvation / transferase activity / metal ion binding
Similarity search - Function
Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
GERANYL S-THIOLODIPHOSPHATE / : / Magnesium-dependent glutamate N-prenyltransferase
Similarity search - Component
Biological speciesPseudo-nitzschia multiseries (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChekan, J.R. / Noel, J.P. / Moore, B.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentNA19NOS4780181 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Algal neurotoxin biosynthesis repurposes the terpene cyclase structural fold into anN-prenyltransferase.
Authors: Chekan, J.R. / McKinnie, S.M.K. / Noel, J.P. / Moore, B.S.
History
DepositionJan 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
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.year
Revision 1.2Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DabA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9794
Polymers51,5701
Non-polymers4103
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.237, 124.237, 114.078
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-606-

HOH

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Components

#1: Protein DabA


Mass: 51569.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudo-nitzschia multiseries (Diatom) / Gene: dabA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A386KZ50
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 4.27 Å3/Da / Density % sol: 71.18 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M sodium citrate 0.05 M HEPES pH 7.5 4 mg/mL DabA was preincubated with 2 mM GSPP, 5 mM MnCl2, and 50 mM L-Glu

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.951 Å / Num. obs: 41688 / % possible obs: 90.9 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.046 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.207 Å / Rmerge(I) obs: 1.133 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 466 / CC1/2: 0.807 / Rpim(I) all: 0.397 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
autoPROCdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→40.991 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.83
RfactorNum. reflection% reflection
Rfree0.2027 1977 4.74 %
Rwork0.1767 --
obs0.1779 41668 90.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.68 Å2 / Biso mean: 35.2388 Å2 / Biso min: 14.9 Å2
Refinement stepCycle: final / Resolution: 2.2→40.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 21 338 3889
Biso mean--48.71 42.02 -
Num. residues----429
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2550.3003620.2431135997
2.255-2.3160.2491340.2324296699
2.316-2.38410.22961550.20943069100
2.3841-2.46110.25181340.2073083100
2.4611-2.5490.25411420.20043104100
2.549-2.65110.24981620.20492845100
2.6511-2.77170.28091230.2236399
2.7717-2.91780.19111570.18953092100
2.9178-3.10050.2271760.1943082100
3.1005-3.33980.19351350.17863137100
3.3398-3.67570.20771170.171230173
3.6757-4.20720.16161540.1451275588
4.2072-5.29880.1571530.13873185100
5.2988-40.9910.19451730.17213350100

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