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- PDB-7smi: Crystal Structure of L-galactose dehydrogenase from Spinacia oleracea -

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Basic information

Entry
Database: PDB / ID: 7smi
TitleCrystal Structure of L-galactose dehydrogenase from Spinacia oleracea
ComponentsL-galactose dehydrogenase
KeywordsPLANT PROTEIN / L-galactose dehydrogenase Enzyme
Function / homology
Function and homology information


L-galactose dehydrogenase activity / L-ascorbic acid biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
L-galactose dehydrogenase-like / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
L-galactose dehydrogenase
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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: Plant Cell.Physiol. / Year: 2022
Title: Structural Characterization of L-Galactose Dehydrogenase: An Essential Enzyme for Vitamin C Biosynthesis.
Authors: Vargas, J.A. / Leonardo, D.A. / D'Muniz Pereira, H. / Lopes, A.R. / Rodriguez, H.N. / Cobos, M. / Marapara, J.L. / Castro, J.C. / Garratt, R.C.
History
DepositionOct 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: L-galactose dehydrogenase


Theoretical massNumber of molelcules
Total (without water)37,6001
Polymers37,6001
Non-polymers00
Water4,161231
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)51.720, 55.071, 61.796
Angle α, β, γ (deg.)90.000, 112.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein L-galactose dehydrogenase


Mass: 37600.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: GDH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): DE3 / References: UniProt: Q6BDJ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

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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: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.32363 Å / Relative weight: 1
ReflectionResolution: 1.4→39.69 Å / Num. obs: 63165 / % possible obs: 99.6 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.04 / Rrim(I) all: 0.146 / Net I/σ(I): 14 / Num. measured all: 804980 / Scaling rejects: 1650
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.4212.11.6323654830240.6430.4851.7052.797.6
7.67-39.69120.08249854160.9970.0240.0863299.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EZI

7ezi


Resolution: 1.4→39.69 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 3182 5.04 %
Rwork0.1933 59964 -
obs0.1942 63146 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.1 Å2 / Biso mean: 20.1183 Å2 / Biso min: 9.32 Å2
Refinement stepCycle: final / Resolution: 1.4→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 0 232 2647
Biso mean---27.15 -
Num. residues----315
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.25651180.24862534265297
1.42-1.440.27111130.2512562267598
1.44-1.470.30621310.24582588271998
1.47-1.490.29751420.23432536267898
1.49-1.520.25761470.2262615276299
1.52-1.550.24881250.21262579270499
1.55-1.580.26161300.20722588271899
1.58-1.610.22631480.206626212769100
1.61-1.650.20891540.205625892743100
1.65-1.690.23881440.202925812725100
1.69-1.740.23361540.198126062760100
1.74-1.790.23931290.198126282757100
1.79-1.850.20871280.200426362764100
1.85-1.910.20711480.19525872735100
1.91-1.990.20681270.185826552782100
1.99-2.080.21851340.18825762710100
2.08-2.190.23491130.17726522765100
2.19-2.330.18771390.186926132752100
2.33-2.510.21991390.192526422781100
2.51-2.760.21141460.202226252771100
2.76-3.160.21741400.203626352775100
3.16-3.980.19661570.182226512808100
3.98-39.690.17031760.173826652841100
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)
11.0751-0.6770.36280.4277-0.20481.6272-0.00270.06940.139-0.09730.0042-0.004-0.1209-0.09110.05720.1741-0.0142-0.0110.1748-0.0070.191813.276827.166142.8604
21.1771-0.26780.3850.77960.06550.971-0.0583-0.01940.04620.07210.03190.1098-0.1059-0.1090.0150.1210.00020.01260.10610.01240.128713.123832.153954.8402
31.0135-0.104-0.04920.8136-0.00670.82480.00640.1492-0.051-0.11480.02320.00430.0320.0425-0.02610.1221-0.0015-0.00430.1192-0.01180.116827.441322.85540.9447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 37 )A5 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 163 )A38 - 163
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 319 )A164 - 319

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