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- PDB-8usu: Crystal Structure of L-galactose 1-dehydrogenase of Myrciaria dub... -

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Basic information

Entry
Database: PDB / ID: 8usu
TitleCrystal Structure of L-galactose 1-dehydrogenase of Myrciaria dubia in complex with NAD
ComponentsL-galactose dehydrogenase isoform X1
KeywordsPLANT PROTEIN / L-galactose 1-dehydrogenase / Enzyme
Function / homologyL-galactose dehydrogenase activity / L-galactose dehydrogenase-like / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-galactose dehydrogenase isoform X1
Function and homology information
Biological speciesMyrciaria dubia (camu-camu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsSantillan, J.A.V. / Cabrejos, D.A.L. / Pereira, H.M. / Gomez, J.C.C. / Garratt, R.C.
Funding support Peru, Brazil, 3items
OrganizationGrant numberCountry
Other government380-2019-BM-INIA-PNIA-PASANTIA Peru
Other governmentCAPES 88887.505769/2020-00 Brazil
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 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-galactose dehydrogenase isoform X1
B: L-galactose dehydrogenase isoform X1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0214
Polymers78,6942
Non-polymers1,3272
Water00
1
A: L-galactose dehydrogenase isoform X1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0102
Polymers39,3471
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L-galactose dehydrogenase isoform X1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0102
Polymers39,3471
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.899, 56.460, 107.392
Angle α, β, γ (deg.)90.00, 109.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein L-galactose dehydrogenase isoform X1


Mass: 39347.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myrciaria dubia (camu-camu) / Gene: LOC115746657 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B8PVT3, EC: 1.1.1.316
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.5 M Ammonium sulfate, 1.0 M lithium sulfate, 0.1 M sodium citrate pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.97→48.4 Å / Num. obs: 14789 / % possible obs: 99.5 % / Redundancy: 6.29 % / CC1/2: 0.959 / Rmerge(I) obs: 0.519 / Rrim(I) all: 0.569 / Net I/σ(I): 4.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.97-3.151.97123230.4332.1541
3.15-3.361.46922270.5881.6031
3.36-3.631.02520910.7731.1191
3.63-3.970.75919070.8360.8351
3.97-4.440.52517220.8860.5791
4.44-5.120.36215610.9240.4021
5.12-6.250.40113250.9360.4391
6.25-8.770.2310230.9860.2481
8.77-48.40.1256100.9880.1361

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→48.4 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 740 5 %
Rwork0.2305 --
obs0.2312 14787 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.97→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4621 0 106 0 4727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024821
X-RAY DIFFRACTIONf_angle_d0.5066564
X-RAY DIFFRACTIONf_dihedral_angle_d12.9461715
X-RAY DIFFRACTIONf_chiral_restr0.041768
X-RAY DIFFRACTIONf_plane_restr0.004835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.20.3421450.30612745X-RAY DIFFRACTION99
3.2-3.520.30591470.27812803X-RAY DIFFRACTION100
3.52-4.030.2441480.25092806X-RAY DIFFRACTION100
4.03-5.070.19091470.20292792X-RAY DIFFRACTION100
5.07-48.40.22051530.18512901X-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)
13.16230.2554-1.18034.03472.44513.48220.36620.07810.2285-0.1482-0.333-0.52780.3641-0.01820.03440.26250.0622-0.08360.35020.09280.249930.90170.431839.8572
27.89853.5468-2.57222.925-3.07845.8915-0.25810.3593-0.7982-1.1849-0.0155-0.45111.45150.07550.18310.46830.05920.00110.355800.332536.7463-11.851635.037
31.4860.6137-0.56630.9197-0.48692.0013-0.06850.127-0.1732-0.13470.11160.05650.1246-0.0215-0.09490.14960.0373-0.07950.3112-0.0390.269329.5261-7.93347.7912
42.1949-0.81130.33482.4682-0.14081.21590.0669-0.1905-0.0156-0.0738-0.05990.0092-0.231-0.0802-0.00950.0918-0.005-0.06230.2548-0.00550.351221.66322.678752.0682
52.55772.0555-0.17434.0457-1.9783.573-0.30110.2956-0.2131-1.1317-0.0347-0.20580.5044-0.44860.11240.9164-0.1381-0.21680.44660.04960.35998.9974-4.373127.8296
63.1525-0.2812-0.59882.2807-1.11580.70270.39570.2514-0.0872-0.7549-0.3198-0.43740.10220.2898-0.10710.33690.1105-0.00360.43880.00430.278423.253.185430.4875
72.6247-0.0007-1.19052.4251-0.93770.85190.44490.51060.1331-0.2678-0.0550.3049-0.1732-0.1686-0.36450.24350.0401-0.07070.428-0.02530.358917.97633.996128.2108
88.17010.17291.50179.7106-5.54333.478-0.035-0.0235-0.0060.0505-0.0674-0.1199-0.05080.05450.09191.2456-0.5488-0.26820.79260.24551.32582.5237-0.498955.5808
91.74321.6022-0.32516.10630.560.53920.0378-0.1461-0.2197-0.467-0.2761-0.2682-0.0390.0110.17220.50110.0318-0.06410.3829-0.01810.346340.0497-23.609121.8029
102.5841.6873-0.17111.50131.04044.4756-0.0583-0.054-0.2984-0.41160.0044-0.9772-0.540.49940.0350.58350.0530.06420.30880.08820.681843.9716-19.22089.8361
111.4573-0.3253-1.57472.5668-0.2152.1889-0.3010.2575-0.1453-1.2098-0.1057-0.82980.31850.2140.25080.89620.10640.31230.37450.06540.580141.8934-30.70621.5574
122.50720.6449-0.56743.6295-1.49973.1883-0.0980.0769-0.1146-0.37310.090.3804-0.0959-0.3032-0.00030.38620.0459-0.0580.2944-0.01420.291724.0735-31.538517.8632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 220 )
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 250 )
6X-RAY DIFFRACTION6chain 'A' and (resid 251 through 278 )
7X-RAY DIFFRACTION7chain 'A' and (resid 279 through 321 )
8X-RAY DIFFRACTION8chain 'A' and (resid 322 through 322 )
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 53 )
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 118 )
11X-RAY DIFFRACTION11chain 'B' and (resid 119 through 187 )
12X-RAY DIFFRACTION12chain 'B' and (resid 188 through 321 )

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