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- PDB-6iuy: Structure of DsGPDH of Dunaliella salina -

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Basic information

Entry
Database: PDB / ID: 6iuy
TitleStructure of DsGPDH of Dunaliella salina
ComponentsGlycerol-3-phosphate dehydrogenase [NAD(+)]
KeywordsOXIDOREDUCTASE / Dehydrogenase Phosphatase / PLANT PROTEIN
Function / homology
Function and homology information


glycerol-3-phosphate dehydrogenase (FAD) complex / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate dehydrogenase (NAD+) activity / glycerol-3-phosphate catabolic process / NADH oxidation / NAD binding / carbohydrate metabolic process / protein homodimerization activity / metal ion binding / cytosol
Similarity search - Function
Glycerol-3-phosphate dehydrogenase, NAD-dependent, eukaryotic / NAD-dependent glycerol-3-phosphate dehydrogenase signature. / Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal / Glycerol-3-phosphate dehydrogenase, NAD-dependent / Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal / NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus / NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / haloacid dehalogenase-like hydrolase ...Glycerol-3-phosphate dehydrogenase, NAD-dependent, eukaryotic / NAD-dependent glycerol-3-phosphate dehydrogenase signature. / Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal / Glycerol-3-phosphate dehydrogenase, NAD-dependent / Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal / NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus / NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glycerol-3-phosphate dehydrogenase [NAD(+)]
Similarity search - Component
Biological speciesDunaliella salina (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHe, Q. / Toh, J.D. / Ero, R. / Qiao, Z. / Kumar, V. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore)MOE2014-T2-1-083 Singapore
CitationJournal: Plant J. / Year: 2020
Title: The unusual di-domain structure of Dunaliella salina glycerol-3-phosphate dehydrogenase enables direct conversion of dihydroxyacetone phosphate to glycerol.
Authors: He, Q. / Toh, J.D. / Ero, R. / Qiao, Z. / Kumar, V. / Serra, A. / Tan, J. / Sze, S.K. / Gao, Y.G.
History
DepositionDec 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly_prop
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _pdbx_struct_assembly_prop.value
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol-3-phosphate dehydrogenase [NAD(+)]
B: Glycerol-3-phosphate dehydrogenase [NAD(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,6639
Polymers137,8552
Non-polymers1,8087
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-53 kcal/mol
Surface area45050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.335, 91.335, 348.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycerol-3-phosphate dehydrogenase [NAD(+)]


Mass: 68927.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dunaliella salina (plant) / Production host: Escherichia coli (E. coli)
References: UniProt: Q52ZA0, glycerol-3-phosphate dehydrogenase (NAD+)

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Non-polymers , 5 types, 372 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.32 % / Description: cubic
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mM NAD+, 10 mM DHAP, 56% Tacsimate pH 7.5 (Hampton)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000021 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000021 Å / Relative weight: 1
ReflectionResolution: 2.2→47.362 Å / Num. obs: 142895 / % possible obs: 99.9 % / Redundancy: 27.913 % / CC1/2: 0.999 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.164 / Χ2: 1.268 / Net I/σ(I): 21.82 / Num. measured all: 3988632
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.3327.4532.161.6963201823115230220.592.20199.6
2.33-2.4926.461.3982.6657456221714217140.7651.425100
2.49-2.6929.1460.8924.5859029020253202530.9130.908100
2.69-2.9529.1710.528.1554185118575185750.9740.529100
2.95-3.328.220.27815.1247424016805168050.9920.283100
3.3-3.826.4490.12433.3439379614889148890.9980.126100
3.8-4.6528.9510.0760.9336212512508125080.9990.071100
4.65-6.5527.3380.05868.182658379724972410.059100
6.55-47.36228.4760.03111.361539135417540510.03199.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WPQ

1wpq


Resolution: 2.2→47.362 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 3808 5 %
Rwork0.199 72336 -
obs0.2014 76144 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.69 Å2 / Biso mean: 53.7861 Å2 / Biso min: 28.16 Å2
Refinement stepCycle: final / Resolution: 2.2→47.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8535 0 178 365 9078
Biso mean--48.42 51.2 -
Num. residues----1116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088813
X-RAY DIFFRACTIONf_angle_d1.18311928
X-RAY DIFFRACTIONf_chiral_restr0.0451326
X-RAY DIFFRACTIONf_plane_restr0.0051548
X-RAY DIFFRACTIONf_dihedral_angle_d16.2733217
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.22790.31531410.28442669
2.2279-2.25720.40371360.29892583
2.2572-2.28810.33821390.27992645
2.2881-2.32080.32341380.25942631
2.3208-2.35540.35751390.26482635
2.3554-2.39220.34131390.2632630
2.3922-2.43150.32571380.25462636
2.4315-2.47340.36911390.24342634
2.4734-2.51840.27681380.24042630
2.5184-2.56680.24971390.23712634
2.5668-2.61920.34711410.23672679
2.6192-2.67610.30481380.22612631
2.6761-2.73840.28071380.2282623
2.7384-2.80680.29161410.2232665
2.8068-2.88270.26791400.21932660
2.8827-2.96750.30631400.22252662
2.9675-3.06330.30291400.20752669
3.0633-3.17280.23611410.22112664
3.1728-3.29980.27661400.22292672
3.2998-3.44990.25941410.20192671
3.4499-3.63170.23621420.19372710
3.6317-3.85920.26081430.18422706
3.8592-4.1570.21591430.17022721
4.157-4.5750.19771440.16162732
4.575-5.23630.20991450.1622751
5.2363-6.59440.22081470.19452806
6.5944-47.360.18541580.17092987

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