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- PDB-3dmt: Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 3dmt
TitleStructure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in complex with the irreversible iodoacetate inhibitor
Components(Glyceraldehyde-3-phosphate dehydrogenase, glycosomal) x 2
KeywordsOXIDOREDUCTASE / ACTIVE-SITE CARBOXYMETHYLATION / IRREVERSIBLE INHIBITOR COMPLEX / TRYPANOSOMA CRUZI / Glycolysis / Glycosome / NAD
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, 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuido, R.V.C. / Balliano, T.L. / Andricopulo, A.D. / Oliva, G.
CitationJournal: Letters in drug design & discovery / Year: 2009
Title: Kinetic and Crystallographic Studies on Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in Complex with Iodoacetate.
Authors: Guido, R.V.C. / Balliano, T.L. / Andricopulo, A.D. / Oliva, G.
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Aug 30, 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
A: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
B: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
C: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
D: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,2549
Polymers156,5084
Non-polymers2,7465
Water18,1051005
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20290 Å2
ΔGint-133 kcal/mol
Surface area45280 Å2
MethodPISA
2
A: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
B: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5524
Polymers78,2252
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-43 kcal/mol
Surface area26630 Å2
MethodPISA
3
C: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
D: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7025
Polymers78,2832
Non-polymers1,4193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-44 kcal/mol
Surface area26640 Å2
MethodPISA
4
A: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
D: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5524
Polymers78,2252
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-35 kcal/mol
Surface area27370 Å2
MethodPISA
5
B: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
C: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7025
Polymers78,2832
Non-polymers1,4193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-36 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.755, 83.713, 105.611
Angle α, β, γ (deg.)90.00, 96.44, 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.: 3
Source method: isolated from a genetically manipulated source
Details: GLYCOSOMAL / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: TcGAP / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GAP-
References: UniProt: P22513, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Protein Glyceraldehyde-3-phosphate dehydrogenase, glycosomal / GAPDH


Mass: 39170.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: carboxymethylated Cys (CCS166) / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: TcGAP / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GAP-
References: UniProt: P22513, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1005 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 18% PEG 8000, 0.1M calcium acetate, 0.1M sodium cacodylate, 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: 1.425 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 12, 2007
RadiationMonochromator: Si curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 2.3→38.9 Å / Num. all: 59362 / Num. obs: 58629 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 2.8
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.135 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX(phenix.refine)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K3T

1k3t


Resolution: 2.3→38.1 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.877 / SU B: 7.156 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.575 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25166 2987 5.1 %RANDOM
Rwork0.1862 ---
obs0.18956 55620 96.48 %-
all-59362 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.905 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.02 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10936 0 182 1005 12123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211345
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.96515422
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6451432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76923.509456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.649151851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6421572
X-RAY DIFFRACTIONr_chiral_restr0.0910.21784
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028436
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.27593
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.27838
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.21480
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.295
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6441.57223
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.091211468
X-RAY DIFFRACTIONr_scbond_it1.63834606
X-RAY DIFFRACTIONr_scangle_it2.5194.53954
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 218 -
Rwork0.193 3830 -
obs--91.65 %

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