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

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Basic information

Entry
Database: PDB / ID: 1jdj
TitleCRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3-PHOSPHATE DEHYDROGENASE IN COMPLEX WITH 2-FLUORO-6-CHLOROPURINE
ComponentsGLYCEROL-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate dehydrogenase (NAD+) activity / glycerol-3-phosphate catabolic process / glycosome / NAD binding / carbohydrate metabolic process / cytosol
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
6-CHLORO-2-FLUOROPURINE / PENTADECANE / Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSuresh, S. / Wisedchaisri, G. / Kennedy, K.J. / Verlinde, C.L.M.J. / Gelb, M.H. / Hol, W.G.J.
CitationJournal: Chem.Biol. / Year: 2002
Title: Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase.
Authors: Choe, J. / Suresh, S. / Wisedchaisri, G. / Kennedy, K.J. / Gelb, M.H. / Hol, W.G.
History
DepositionJun 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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: GLYCEROL-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7033
Polymers39,3181
Non-polymers3852
Water2,882160
1
A: GLYCEROL-3-PHOSPHATE DEHYDROGENASE
hetero molecules

A: GLYCEROL-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4066
Polymers78,6362
Non-polymers7704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7750 Å2
ΔGint-47 kcal/mol
Surface area25990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.3, 70.3, 210.9
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212
Detailsbiological dimer generated by crystallographic 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) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P90551, glycerol-3-phosphate dehydrogenase (NAD+)
#2: Chemical ChemComp-CFP / 6-CHLORO-2-FLUOROPURINE


Mass: 172.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H2ClFN4
#3: Chemical ChemComp-MYS / PENTADECANE


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


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.9 M sodium citrate, 50 mM TEA pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 0.8-0.9 M / Common name: sodium citrate

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 27686 / Num. obs: 27686 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.08 % / Biso Wilson estimate: 28.44 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 27
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 7.6 / Num. unique all: 2492 / Rsym value: 0.184 / % possible all: 91.6
Reflection
*PLUS
Redundancy: 7.1 % / Num. measured all: 196124
Reflection shell
*PLUS
% possible obs: 91.6 % / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EVY

1evy


Resolution: 2.2→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS / Details: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1364 -RANDOM
Rwork0.208 ---
all0.208 27686 --
obs0.208 27686 99.1 %-
Displacement parametersBiso mean: 31.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 26 160 2791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.14
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.248 124 -
Rwork0.215 --
obs-2492 91.6 %
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Rfactor obs: 0.215

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