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- PDB-1txg: Structure of glycerol-3-phosphate dehydrogenase from Archaeoglobu... -

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Basic information

Entry
Database: PDB / ID: 1txg
TitleStructure of glycerol-3-phosphate dehydrogenase from Archaeoglobus fulgidus
Componentsglycerol-3-phosphate dehydrogenase [NAD(P)+]
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


glycerol-3-phosphate dehydrogenase (NADP+) activity / glycerophospholipid metabolic process / glycerol-3-phosphate catabolic process / glycerol-3-phosphate biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / NAD binding / carbohydrate metabolic process / cytosol
Similarity search - Function
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 ...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
AMMONIUM ION / NADP(+)-dependent glycerol-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
AuthorsSakasegawa, S. / Hagemeier, C.H. / Thauer, R.K. / Essen, L.O. / Shima, S.
CitationJournal: Protein Sci. / Year: 2004
Title: Structural and functional analysis of the gpsA gene product of Archaeoglobus fulgidus: A glycerol-3-phosphate dehydrogenase with an unusual NADP+ preference
Authors: Sakasegawa, S. / Hagemeier, C.H. / Thauer, R.K. / Essen, L.O. / Shima, S.
History
DepositionJul 5, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 1, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_close_contact ...database_2 / pdbx_validate_close_contact / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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(P)+]
B: glycerol-3-phosphate dehydrogenase [NAD(P)+]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,62113
Polymers73,6512
Non-polymers97111
Water13,565753
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-116 kcal/mol
Surface area25390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.223, 67.586, 81.156
Angle α, β, γ (deg.)90.00, 106.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: 1 - 335 / Label seq-ID: 1 - 335

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe dimer in the asymmetric unit is the biological assembly

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Components

#1: Protein glycerol-3-phosphate dehydrogenase [NAD(P)+] / NADP / H-dependent glycerol-3-phosphate dehydrogenase


Mass: 36825.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pEGPD1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: O29390, glycerol-3-phosphate dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 282K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→17 Å / Num. obs: 63641

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→16.98 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.995 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 3438 5.1 %RANDOM
Rwork0.14931 ---
obs0.1515 63641 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å2-0.42 Å2
2---0.03 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→16.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5172 0 53 753 5978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225314
X-RAY DIFFRACTIONr_bond_other_d0.0020.025052
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9857180
X-RAY DIFFRACTIONr_angle_other_deg0.894311714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2095668
X-RAY DIFFRACTIONr_chiral_restr0.1110.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025804
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021042
X-RAY DIFFRACTIONr_nbd_refined0.2320.21175
X-RAY DIFFRACTIONr_nbd_other0.2460.26039
X-RAY DIFFRACTIONr_nbtor_other0.0840.23096
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2537
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3660.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.234
X-RAY DIFFRACTIONr_mcbond_it0.991.53310
X-RAY DIFFRACTIONr_mcangle_it1.84425340
X-RAY DIFFRACTIONr_scbond_it3.1432004
X-RAY DIFFRACTIONr_scangle_it4.9584.51840
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5118 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.525
loose thermal2.7210
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 241
Rwork0.232 4391

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