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- PDB-1qxs: CRYSTAL STRUCTURE OF Trypanosoma cruzi GLYCERALDEHYDE-3- PHOSPHAT... -

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Basic information

Entry
Database: PDB / ID: 1qxs
TitleCRYSTAL STRUCTURE OF Trypanosoma cruzi GLYCERALDEHYDE-3- PHOSPHATE DEHYDROGENASE COMPLEXED WITH AN ANALOGUE OF 1,3- BisPHOSPHO-D-GLYCERIC ACID
ComponentsGlyceraldehyde 3-phosphate dehydrogenase, glycosomal
KeywordsOXIDOREDUCTASE / gGAPDH 1 / 3-BPGA analogue complex
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycosome / 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 / Chem-S70 / Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsCastilho, M.S. / Pavao, F. / Oliva, G.
CitationJournal: Eur.J.Biochem. / Year: 2003
Title: Crystal structure of Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase complexed with an analogue of 1,3-bisphospho-d-glyceric acid.
Authors: Ladame, S. / Castilho, M.S. / Silva, C.H. / Denier, C. / Hannaert, V. / Perie, J. / Oliva, G. / Willson, M.
History
DepositionSep 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 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
C: Glyceraldehyde 3-phosphate dehydrogenase, glycosomal
D: Glyceraldehyde 3-phosphate dehydrogenase, glycosomal
A: Glyceraldehyde 3-phosphate dehydrogenase, glycosomal
B: Glyceraldehyde 3-phosphate dehydrogenase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3689
Polymers156,4504
Non-polymers2,9185
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20500 Å2
ΔGint-133 kcal/mol
Surface area47020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.756, 85.195, 106.421
Angle α, β, γ (deg.)90.00, 96.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glyceraldehyde 3-phosphate dehydrogenase, glycosomal / GAPDH


Mass: 39112.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: P22513, 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: Chemical ChemComp-S70 / 3-HYDROXY-2-OXO-4-PHOPHONOXY- BUTYL)-PHOSPHONIC ACID


Mass: 264.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O9P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M sodium cacodylate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 4, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 33574 / Num. obs: 31898 / % possible obs: 92.41 %
Reflection shellHighest resolution: 2.75 Å / % possible all: 92.41

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→8 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.874 / SU B: 17.042 / SU ML: 0.344 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27644 1670 5 %RANDOM
Rwork0.19762 ---
all0.207 33754 --
obs0.20158 31898 92.41 %-
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: 56.626 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å2-5.12 Å2
2---3.46 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 191 453 11576
LS refinement shellResolution: 2.75→2.813 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 107 -
Rwork0.295 2169 -
obs-31898 92.41 %

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