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- PDB-4fgw: Structure of Glycerol-3-Phosphate Dehydrogenase, GPD1, from Sacha... -

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Basic information

Entry
Database: PDB / ID: 4fgw
TitleStructure of Glycerol-3-Phosphate Dehydrogenase, GPD1, from Sacharomyces Cerevisiae
ComponentsGlycerol-3-phosphate dehydrogenase [NAD(+)] 1
KeywordsOXIDOREDUCTASE / Dehydrogenase / NAD+
Function / homology
Function and homology information


intracellular accumulation of glycerol / Synthesis of PA / glycerol-3-phosphate dehydrogenase [NAD(P)+] activity => GO:0047952 / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate metabolic process / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / protein import into peroxisome matrix / NADH oxidation / peroxisome ...intracellular accumulation of glycerol / Synthesis of PA / glycerol-3-phosphate dehydrogenase [NAD(P)+] activity => GO:0047952 / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate metabolic process / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / protein import into peroxisome matrix / NADH oxidation / peroxisome / NAD binding / carbohydrate metabolic process / protein homodimerization activity / mitochondrion / nucleus / 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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glycerol-3-phosphate dehydrogenase [NAD(+)] 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Phaser / Resolution: 2.45 Å
AuthorsAparicio, D. / Munmun, N. / Carpena, X. / Fita, I. / Loewen, P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of glycerol-3-phosphate dehydrogenase (GPD1) from Saccharomyces cerevisiae at 2.45A resolution
Authors: Alarcon, D.A. / Nandi, M. / Carpena, X. / Fita, I. / Loewen, P.C.
History
DepositionJun 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 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(+)] 1
B: Glycerol-3-phosphate dehydrogenase [NAD(+)] 1


Theoretical massNumber of molelcules
Total (without water)85,8312
Polymers85,8312
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-13 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.420, 64.420, 198.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 42915.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GPD1, DAR1, HOR1, OSG1, YDL022W, D2830 / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q00055, glycerol-3-phosphate dehydrogenase (NAD+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% Polyethylene Glycol 8000, 0.1 M Tris-HCl pH 8.5 and 0.3 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.45→29.4 Å / Num. all: 29348 / Num. obs: 29348 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 67.4 Å2 / Rsym value: 0.036 / Net I/σ(I): 14.24
Reflection shellResolution: 2.45→2.51 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.05 / Num. unique all: 2152 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: Phaser
Starting model: PDB entry 1X0V

1x0v


Resolution: 2.45→29.4 Å / Cor.coef. Fo:Fc: 0.9407 / Cor.coef. Fo:Fc free: 0.9382 / SU R Cruickshank DPI: 0.426 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1492 5.08 %RANDOM
Rwork0.1996 ---
all0.21 29348 --
obs0.2 29348 99.27 %-
Displacement parametersBiso mean: 83.78 Å2
Baniso -1Baniso -2Baniso -3
1-4.2029 Å20 Å20 Å2
2--4.2029 Å20 Å2
3----8.4057 Å2
Refine analyzeLuzzati coordinate error obs: 0.479 Å
Refinement stepCycle: LAST / Resolution: 2.45→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5462 0 0 54 5516
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085582HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.197576HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1906SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes806HARMONIC5
X-RAY DIFFRACTIONt_it5582HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion20.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion728SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6439SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.54 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2177 143 5.27 %
Rwork0.1982 2572 -
all0.1992 2715 -
obs--99.27 %
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)
14.21310.58630.65463.86971.49493.04480.06450.5871-0.5442-0.6884-0.36920.30920.0189-0.61250.30470.08980.0444-0.1044-0.0073-0.2278-0.119614.2953-15.6651-19.2026
22.8610.31010.76644.96610.44523.2142-0.2751-0.19890.818-0.13-0.1102-1.0101-0.48080.36340.3852-0.0376-0.0083-0.2026-0.1216-0.03070.326135.457910.3296-2.2032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A33 - 385
2X-RAY DIFFRACTION2{ B|* }B33 - 385

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