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- PDB-3v1y: Crystal structures of glyceraldehyde-3-phosphate dehydrogenase co... -

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Basic information

Entry
Database: PDB / ID: 3v1y
TitleCrystal structures of glyceraldehyde-3-phosphate dehydrogenase complexes with NAD
ComponentsGlyceraldehyde-3-phosphate dehydrogenase, cytosolic
KeywordsOXIDOREDUCTASE / Rossmann Fold / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / NAD(H) Binding
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, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsTien, Y.C. / Chuankhayan, P. / Lin, Y.H. / Chang, S.L. / Chen, C.J.
CitationJournal: Plant Mol.Biol. / Year: 2012
Title: Crystal structures of rice (Oryza sativa) glyceraldehyde-3-phosphate dehydrogenase complexes with NAD and sulfate suggest involvement of Phe37 in NAD binding for catalysis
Authors: Tien, Y.C. / Chuankhayan, P. / Huang, Y.C. / Chen, C.D. / Alikhajeh, J. / Chang, S.L. / Chen, C.J.
History
DepositionDec 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)148,4888
Polymers145,8344
Non-polymers2,6544
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19750 Å2
ΔGint-138 kcal/mol
Surface area45010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.171, 128.173, 77.314
Angle α, β, γ (deg.)90.00, 117.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36458.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: GAPC, GPC, Os08g0126300, LOC_Os08g03290, OJ1163_G08.15, OsJ_024858
Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: Q0J8A4, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 16% PEG 3350 (w/v), 0.1M citric acid pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. all: 108982 / Num. obs: 108982 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 %

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→30 Å / Occupancy max: 1 / Occupancy min: 0.3 / σ(F): 1.8 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 10390 9.4 %RANDOM
Rwork0.234 ---
all0.267 103808 --
obs0.267 103808 --
Solvent computationBsol: 43.4567 Å2
Displacement parametersBiso max: 75.67 Å2 / Biso mean: 16.6646 Å2 / Biso min: 1.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.385 Å20 Å20.268 Å2
2--3.43 Å20 Å2
3----3.815 Å2
Refinement stepCycle: LAST / Resolution: 1.86→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10212 0 176 329 10717
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2NAD.param

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