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- PDB-7sml: Crystal Structure of L-GALACTONO-1,4-LACTONE DEHYDROGENASE de Myr... -

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Basic information

Entry
Database: PDB / ID: 7sml
TitleCrystal Structure of L-GALACTONO-1,4-LACTONE DEHYDROGENASE de Myrciaria dubia
ComponentsL-GALACTONO-1,4-LACTONE DEHYDROGENASE
KeywordsPLANT PROTEIN / L-GALACTONO-1 / 4-LACTONE DEHYDROGENASE / Enzyme
Biological speciesMyrciaria dubia (camu-camu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSantillan, J.A.V. / Cabrejos, D.A.L. / Pereira, H.M. / Gomez, J.C.C. / Garratt, R.C.
Funding support Peru, 2items
OrganizationGrant numberCountry
Other government188-2018-INIA-PNIA-PASANTIA
Other government069-2019-FONDECYT Peru
CitationJournal: J.Exp.Bot. / Year: 2024
Title: Structural insights into the Smirnoff-Wheeler pathway for vitamin C production in the Amazon fruit Camu-Camu.
Authors: Vargas, J.A. / Sculaccio, S.A. / Pinto, A.P.A. / Pereira, H.D. / Mendes, L.F.S. / Flores, J.F. / Cobos, M. / Castro, J.C. / Garratt, R.C. / Leonardo, D.A.
History
DepositionOct 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-GALACTONO-1,4-LACTONE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)61,5691
Polymers61,5691
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.157, 79.089, 89.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein L-GALACTONO-1,4-LACTONE DEHYDROGENASE


Mass: 61568.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myrciaria dubia (camu-camu) / Plasmid: pET151_D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): DE3 / References: L-galactonolactone dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SPG (succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7); pH 7.0 and 25 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRUS / Beamline: MANACA / Wavelength: 1.32363 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.32363 Å / Relative weight: 1
ReflectionResolution: 2.1→44.97 Å / Num. obs: 27421 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.225 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 13.7 % / Rmerge(I) obs: 2.469 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALPHAFOLD

Resolution: 2.1→43.58 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 1419 5.18 %
Rwork0.206 --
obs0.208 27376 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 0 145 3796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.32781460.2982540X-RAY DIFFRACTION100
2.18-2.260.29331470.26632546X-RAY DIFFRACTION100
2.26-2.370.26961490.25082551X-RAY DIFFRACTION100
2.37-2.490.30361530.24112545X-RAY DIFFRACTION100
2.49-2.650.25421330.22962571X-RAY DIFFRACTION100
2.65-2.850.27971450.21682573X-RAY DIFFRACTION100
2.85-3.140.25261410.21992592X-RAY DIFFRACTION100
3.14-3.590.23511320.19792620X-RAY DIFFRACTION100
3.59-4.520.22171360.1792635X-RAY DIFFRACTION100
4.52-43.580.20871370.18422784X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6851-1.46090.18472.1120.08710.96320.0638-0.0156-0.0918-0.2067-0.09280.2107-0.0765-0.0613-0.01480.31250.00370.02430.34860.01810.37521.35849.544628.0094
21.8872-0.00270.6311.42550.13591.25980.0235-0.19810.07170.1212-0.0308-0.1345-0.0138-0.00570.02240.20630.01840.01410.25210.01970.219843.459159.273835.5785
30.2968-0.6460.58861.302-1.28331.3064-0.1776-0.3986-0.08980.43040.20380.03160.11280.0461-0.08770.41160.06240.02940.37450.04230.283242.397657.417936.149
41.33710.10040.29251.71730.57891.8039-0.03310.13390.1457-0.3677-0.0287-0.0664-0.28860.05030.0430.33010.02540.03150.25860.03610.252239.710666.98420.1778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 24 THROUGH 119 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 120 THROUGH 320 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 321 THROUGH 349 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 350 THROUGH 502 )

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