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- PDB-1a7k: GLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A MONOCLIN... -

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Basic information

Entry
Database: PDB / ID: 1a7k
TitleGLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A MONOCLINIC CRYSTAL FORM
ComponentsGLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASEGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / GLYCOSOME / TRYPANOSOME
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
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 / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKim, H. / Hol, W.G.J.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of Leishmania mexicana glycosomal glyceraldehyde-3-phosphate dehydrogenase in a new crystal form confirms the putative physiological active site structure.
Authors: Kim, H. / Hol, W.G.
#1: Journal: Biochemistry / Year: 1995
Title: Crystal Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Leishmania Mexicana: Implications for Structure-Based Drug Design and a New Position for the Inorganic Phosphate Binding Site
Authors: Kim, H. / Feil, I.K. / Verlinde, C.L. / Petra, P.H. / Hol, W.G.
History
DepositionMar 16, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
C: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
D: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,22716
Polymers155,8144
Non-polymers3,41312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22160 Å2
ΔGint-200 kcal/mol
Surface area45050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.900, 81.000, 131.900
Angle α, β, γ (deg.)90.00, 95.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999472, 0.030711, -0.010656), (0.027818, 0.638457, -0.769155), (-0.016818, -0.769044, -0.638974)
Vector: 93.23406, 107.34053, 232.33264)

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Components

#1: Protein
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / Glyceraldehyde 3-phosphate dehydrogenase / GAPDH


Mass: 38953.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ONE BOUND NAD AND TWO BOUND PHOSPHATES PER MONOMER / Source: (gene. exp.) Leishmania mexicana (eukaryote) / Cell line: BL21 / Plasmid: PET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS
References: UniProt: Q27890, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

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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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growMethod: vapor diffusion / pH: 7
Details: VAPOR DIFFUSION: 100 MM SODIUM PHOSPHATE, 27.5% PEG-1000 PH 7.0 (PH ADJUSTED WITH 100 MM CITRIC ACID), vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
2100 mMtriethanolamine1drop
3200 mM1dropKCl
41 mMdithiothreitol1drop
51 mMEDTA1drop
6100 mMsodium phosphate1reservoir
727.5 %PEG10001reservoir
8100 mMcitric acid1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 2, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 28710 / % possible obs: 81 % / Redundancy: 2.5 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.071
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.481 / % possible all: 81
Reflection
*PLUS
Num. measured all: 78266 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 81 % / Rmerge(I) obs: 0.481

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRYPANOSOMA BRUCEI GAPDH

Resolution: 2.8→8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1343 5 %RANDOM
Rwork0.217 ---
obs0.217 27607 81 %-
Displacement parametersBiso mean: 49 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10864 0 216 0 11080
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellHighest resolution: 2.8 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.42 150 4 %
Rwork0.338 3227 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Rfactor obs: 0.338

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