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- PDB-1evz: CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3-PHOSPHATE DEH... -

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Basic information

Entry
Database: PDB / ID: 1evz
TitleCRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3-PHOSPHATE DEHYDROGENASE IN COMPLEX WITH NAD
ComponentsGLYCEROL-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / Dehydrogenase / Rossmann fold
Function / homology
Function and homology information


glycerol-3-phosphate dehydrogenase [NAD(P)+] activity / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / glycosome / NAD binding / carbohydrate metabolic process
Similarity search - Function
NAD-dependent glycerol-3-phosphate dehydrogenase signature. / Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal / Glycerol-3-phosphate dehydrogenase, NAD-dependent / Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal / NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus / NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily ...NAD-dependent glycerol-3-phosphate dehydrogenase signature. / Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal / Glycerol-3-phosphate dehydrogenase, NAD-dependent / Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal / NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus / NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PENTADECANE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsSuresh, S. / Turley, S. / Opperdoes, F.R. / Michels, P.A.M. / Hol, W.G.J.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana.
Authors: Suresh, S. / Turley, S. / Opperdoes, F.R. / Michels, P.A. / Hol, W.G.
History
DepositionApr 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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: GLYCEROL-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1943
Polymers39,3181
Non-polymers8762
Water1,44180
1
A: GLYCEROL-3-PHOSPHATE DEHYDROGENASE
hetero molecules

A: GLYCEROL-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3876
Polymers78,6362
Non-polymers1,7524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9270 Å2
ΔGint-56 kcal/mol
Surface area24980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.850, 69.850, 211.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

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Components

#1: Protein GLYCEROL-3-PHOSPHATE DEHYDROGENASE /


Mass: 39317.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Cellular location: GLYCOSOME / Plasmid: PET3 / Production host: Escherichia coli (E. coli)
References: UniProt: P90551, glycerol-3-phosphate dehydrogenase (NAD+)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MYS / PENTADECANE / Pentadecane


Mass: 212.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.29 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: Triethanol amine pH 7.25 Sodium Citrate 0.9M, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein1drop
220 mMTEA1drop
34 mMNAD1drop
44 mMdithiothreitol1drop
51 mMEDTA1drop
60.2 mMPMSF1drop
70.9 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 13746 / Num. obs: 13000 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 55.207 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 27.63
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.183 / Num. unique all: 1341 / % possible all: 100
Reflection
*PLUS
Num. measured all: 93667
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: TNT
RfactorNum. reflectionSelection details
Rfree0.255 692 random
Rwork0.183 --
all0.183 13746 -
obs0.183 13000 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 59 80 2741
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.23
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.93 Å / Rfactor Rfree: 0.4 / Rfactor obs: 0.27

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