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- PDB-3e6a: Crystal structure and Functional Analysis of Glyceraldehyde-3-pho... -

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Basic information

Entry
Database: PDB / ID: 3e6a
TitleCrystal structure and Functional Analysis of Glyceraldehyde-3-phosphate Dehydrogenase from Oryza Sativa
ComponentsGlyceraldehyde-3-phosphate dehydrogenase, cytosolic
KeywordsOXIDOREDUCTASE / GAPDH / Glyceraldehyde-3-phosphate / Oryza Sativa / rice / sulfate / Cytoplasm / Glycolysis / NAD
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.77 Å
AuthorsTien, Y.C. / Lin, Y.H. / Chang, S.L. / Chen, C.J.
CitationJournal: To be Published
Title: Crystal structure and Functional Analysis of Glyceraldehyde-3-phosphate Dehydrogenase from Oryza Sativa
Authors: Tien, Y.C. / Lin, Y.H. / Chang, S.L. / Chen, C.J.
History
DepositionAug 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase, cytosolic
A: Glyceraldehyde-3-phosphate dehydrogenase, cytosolic
B: Glyceraldehyde-3-phosphate dehydrogenase, cytosolic
C: Glyceraldehyde-3-phosphate dehydrogenase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,07812
Polymers145,3104
Non-polymers7698
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16280 Å2
ΔGint-204 kcal/mol
Surface area46300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.258, 127.418, 77.385
Angle α, β, γ (deg.)90.00, 118.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase, cytosolic / PP38


Mass: 36327.406 Da / Num. of mol.: 4 / Fragment: ligand binding
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Strain: Japonica cultivar-group / Gene: GAPDH / Plasmid: pET-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0J8A4, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.05M Ammonium sulfate, 0.05M Bis-Tris, 40% (w/v) 15/4 EO/OH, pH 6.1, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.77→30 Å / Num. obs: 16104 / % possible obs: 99.1 % / Redundancy: 7.6 % / Rsym value: 0.325

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 3.77→30 Å / Occupancy max: 1 / Occupancy min: 0.3
RfactorNum. reflection% reflection
Rfree0.21 --
Rwork0.196 --
obs-16104 99.1 %
Displacement parametersBiso max: 0.85 Å2 / Biso mean: 0.061 Å2 / Biso min: 0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10171 0 40 101 10312
LS refinement shellResolution: 3.77→3.99 Å
RfactorNum. reflection% reflection
Rfree0.21 --
Rwork0.196 --
obs-2120 99.1 %

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