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- PDB-7zhy: Leishmania donovani Glucose 6-Phosphate Dehydrogenase C138S mutan... -

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Basic information

Entry
Database: PDB / ID: 7zhy
TitleLeishmania donovani Glucose 6-Phosphate Dehydrogenase C138S mutant complexed with NADP(H)
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Trypanosoma / Leishmania donovani / Glucose 6-Phosphate Dehydrogenase / G6P / NADP(H) / pentose phosphate pathway
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt / glucose metabolic process / NADP binding
Similarity search - Function
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsFritz-Wolf, K. / Berneburg, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
LOEWE Center DRUID (Novel Drug Targets against Poverty-related and Neglected Tropical Infectious Diseases)Project B3 and E3 Germany
CitationJournal: Commun Biol / Year: 2022
Title: Crystal structure of Leishmania donovani glucose 6-phosphate dehydrogenase reveals a unique N-terminal domain.
Authors: Berneburg, I. / Rahlfs, S. / Becker, K. / Fritz-Wolf, K.
History
DepositionApr 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,36645
Polymers126,7842
Non-polymers4,58243
Water13,565753
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16670 Å2
ΔGint-27 kcal/mol
Surface area45060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.170, 65.690, 119.930
Angle α, β, γ (deg.)90.000, 120.750, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucose-6-phosphate 1-dehydrogenase


Mass: 63391.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: g6pdh / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A2CIL3, glucose-6-phosphate dehydrogenase (NADP+)

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Non-polymers , 6 types, 796 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 10 % PEG 3000 and 100-150 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.99→47.96 Å / Num. obs: 102119 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 40.25 Å2 / CC1/2: 1 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 10084 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292122100

Resolution: 1.99→47.95 Å / SU ML: 0.2937 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2187 10209 10 %
Rwork0.1835 91862 -
obs0.187 102071 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.02 Å2
Refinement stepCycle: LAST / Resolution: 1.99→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8424 0 288 753 9465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01958922
X-RAY DIFFRACTIONf_angle_d1.072112031
X-RAY DIFFRACTIONf_chiral_restr0.05941310
X-RAY DIFFRACTIONf_plane_restr0.00811542
X-RAY DIFFRACTIONf_dihedral_angle_d13.37831246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.010.46233310.43312985X-RAY DIFFRACTION98.43
2.01-2.040.41443400.37323060X-RAY DIFFRACTION99.53
2.04-2.060.34453360.33123024X-RAY DIFFRACTION99.59
2.06-2.090.32643360.28473024X-RAY DIFFRACTION99.61
2.09-2.120.28053440.23653090X-RAY DIFFRACTION99.8
2.12-2.140.24853340.22953001X-RAY DIFFRACTION99.85
2.14-2.180.29843400.23513071X-RAY DIFFRACTION99.8
2.18-2.210.27623370.22873038X-RAY DIFFRACTION99.73
2.21-2.240.38133400.28213054X-RAY DIFFRACTION99.5
2.24-2.280.36993410.30843067X-RAY DIFFRACTION99.33
2.28-2.320.24283350.19683015X-RAY DIFFRACTION99.82
2.32-2.360.25713430.19923093X-RAY DIFFRACTION99.97
2.36-2.410.24053370.20863029X-RAY DIFFRACTION99.76
2.41-2.460.24683380.19523041X-RAY DIFFRACTION99.79
2.46-2.510.24973410.19833067X-RAY DIFFRACTION99.8
2.51-2.570.2493400.19743059X-RAY DIFFRACTION99.77
2.57-2.630.25273420.18563076X-RAY DIFFRACTION99.71
2.63-2.70.24313410.18363062X-RAY DIFFRACTION99.94
2.7-2.780.24893410.17583067X-RAY DIFFRACTION99.85
2.78-2.870.21683390.17863052X-RAY DIFFRACTION99.71
2.87-2.970.22793420.17933083X-RAY DIFFRACTION99.65
2.97-3.090.2213370.18173028X-RAY DIFFRACTION99.62
3.09-3.230.22523440.18433100X-RAY DIFFRACTION99.62
3.23-3.40.20953400.17483052X-RAY DIFFRACTION99.59
3.4-3.620.2183420.17323085X-RAY DIFFRACTION99.33
3.62-3.90.1993380.16993042X-RAY DIFFRACTION98.86
3.9-4.290.17763430.15273089X-RAY DIFFRACTION99.54
4.29-4.910.15763440.13383088X-RAY DIFFRACTION99.48
4.91-6.180.18483460.16683122X-RAY DIFFRACTION99.54

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