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- PDB-1ywg: The structure of glyceraldehyde-3-phosphate dehydrogenase from Pl... -

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Basic information

Entry
Database: PDB / ID: 1ywg
TitleThe structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum
Componentsglyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / Dehydrogenase / Tetrameric
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
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
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSatchell, J.F. / Klonis, N. / Malby, R.L. / Adisa, A. / Alpyurek, A.E. / Colman, P.M. / Tilley, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum.
Authors: Satchell, J.F. / Malby, R.L. / Luo, C.S. / Adisa, A. / Alpyurek, A.E. / Klonis, N. / Smith, B.J. / Tilley, L. / Colman, P.M.
History
DepositionFeb 17, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
P: glyceraldehyde-3-phosphate dehydrogenase
Q: glyceraldehyde-3-phosphate dehydrogenase
R: glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3788
Polymers146,7254
Non-polymers2,6544
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19430 Å2
ΔGint-129 kcal/mol
Surface area44940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.600, 79.600, 406.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
glyceraldehyde-3-phosphate dehydrogenase / GAPDH


Mass: 36681.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: 3D7 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8T6B1, 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.: 314 / 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: 2.6 Å3/Da / Density % sol: 51.412247 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.2M Calcium acetate, 20%(w/v) polyethylene glycol 3350, 1mM NAD, 10mg/ml GAPDH, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2004
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator for Sagittal focusing. Dynamically bendable mirror for Meridional focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 44608 / Num. obs: 44207 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 53.7 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 9.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2 / Num. unique all: 4232 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GD1

1gd1


Resolution: 2.6→29.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 72348.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: least squares and simulated annealing protocols using the maximum likelihood target implemented in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2187 5 %RANDOM
Rwork0.231 ---
all0.232 44207 --
obs0.231 44164 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.9486 Å2 / ksol: 0.314783 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.68 Å24.52 Å20 Å2
2--8.68 Å20 Å2
3----17.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10164 0 176 314 10654
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.454
X-RAY DIFFRACTIONc_scangle_it2.135
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 385 5.4 %
Rwork0.3 6798 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NAD.PARAMNAD.TOP

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