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

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Basic information

Entry
Database: PDB / ID: 6vkz
TitleCrystal Structure of the N-prenyltransferase DabA in Complex with GSPP and Mg2+
ComponentsDabA
KeywordsTRANSFERASE / prenyltransferase / terpene cyclase
Function / homologycellular response to carbon dioxide / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Terpene synthase family 2, C-terminal metal binding / cellular response to phosphate starvation / Isoprenoid synthase domain superfamily / transferase activity / metal ion binding / GERANYL S-THIOLODIPHOSPHATE / Magnesium-dependent glutamate N-prenyltransferase
Function and homology information
Biological speciesPseudo-nitzschia multiseries (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DabA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9494
Polymers51,5701
Non-polymers3793
Water7,026390
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)124.286, 124.286, 114.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11A-850-

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 4.29 Å3/Da / Density % sol: 71.31 %
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 preincubated with 2 mM GSPP, 5 mM MgCl2, 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: 2.1→42.102 Å / Num. obs: 50088 / % possible obs: 94.9 % / Redundancy: 11.8 % / Biso Wilson estimate: 27.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.039 / Net I/σ(I): 16.6
Reflection shellResolution: 2.1→2.107 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.194 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 526 / CC1/2: 0.776 / Rpim(I) all: 0.359 / % 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: 2.1→42.1 Å / SU ML: 0.1584 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1877 2560 5.11 %
Rwork0.1662 47504 -
obs0.1674 50064 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 21 390 3941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653711
X-RAY DIFFRACTIONf_angle_d0.77145044
X-RAY DIFFRACTIONf_chiral_restr0.0452545
X-RAY DIFFRACTIONf_plane_restr0.0053650
X-RAY DIFFRACTIONf_dihedral_angle_d15.06472277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.26011490.22372735X-RAY DIFFRACTION100
2.14-2.180.24311630.20642706X-RAY DIFFRACTION100
2.18-2.230.23921370.2022504X-RAY DIFFRACTION93.62
2.23-2.280.2676740.2111275X-RAY DIFFRACTION89.63
2.28-2.340.20331300.1832768X-RAY DIFFRACTION100
2.34-2.40.2061250.18012755X-RAY DIFFRACTION100
2.4-2.470.19241100.17262786X-RAY DIFFRACTION100
2.47-2.550.22121390.16982784X-RAY DIFFRACTION100
2.55-2.650.19081460.17442727X-RAY DIFFRACTION99.24
2.65-2.750.20111280.18381876X-RAY DIFFRACTION68.91
2.75-2.880.21931400.18082776X-RAY DIFFRACTION100
2.88-3.030.21141320.1842804X-RAY DIFFRACTION100
3.03-3.220.19071520.16492761X-RAY DIFFRACTION100
3.22-3.470.17561550.16432802X-RAY DIFFRACTION100
3.47-3.820.17121670.14512788X-RAY DIFFRACTION100
3.82-4.370.16181740.1332798X-RAY DIFFRACTION100
4.37-5.50.15161790.14222837X-RAY DIFFRACTION100
5.5-42.10.18651600.17613022X-RAY DIFFRACTION99.84

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