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- PDB-7zhz: Leishmania donovani Glucose 6-Phosphate Dehydrogenase mutant C138... -

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Basic information

Entry
Database: PDB / ID: 7zhz
TitleLeishmania donovani Glucose 6-Phosphate Dehydrogenase mutant C138S complexed with G6P and 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, oxidative branch / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-glucopyranose / Chem-NDP / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)129,45516
Polymers126,7842
Non-polymers2,67214
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-124 kcal/mol
Surface area45660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.160, 66.020, 120.020
Angle α, β, γ (deg.)90.000, 120.731, 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 / Sugars , 2 types, 3 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 (E. coli)
References: UniProt: A2CIL3, glucose-6-phosphate dehydrogenase (NADP+)
#5: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 38 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.: 4 / 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 10 % PEG 3000, 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: 2.5→48.8 Å / Num. obs: 51043 / % possible obs: 99.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 75.57 Å2 / CC1/2: 1 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 5069 / 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: 2.5→48.75 Å / SU ML: 0.528 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.3212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2979 5096 10.01 %
Rwork0.2492 45813 -
obs0.2541 50909 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.18 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8344 0 163 25 8532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00278674
X-RAY DIFFRACTIONf_angle_d0.664911743
X-RAY DIFFRACTIONf_chiral_restr0.04431289
X-RAY DIFFRACTIONf_plane_restr0.00451506
X-RAY DIFFRACTIONf_dihedral_angle_d9.99591171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.55381700.54081524X-RAY DIFFRACTION98.89
2.53-2.560.49341650.50151488X-RAY DIFFRACTION99.04
2.56-2.590.46471680.47311515X-RAY DIFFRACTION98.54
2.59-2.620.48251680.44071504X-RAY DIFFRACTION99.41
2.62-2.660.4411700.40481520X-RAY DIFFRACTION99.47
2.66-2.690.46081680.37721500X-RAY DIFFRACTION99.4
2.69-2.730.40641690.36841526X-RAY DIFFRACTION99.47
2.73-2.770.40861670.31981503X-RAY DIFFRACTION99.05
2.77-2.820.35751670.31541515X-RAY DIFFRACTION99.64
2.82-2.860.35031730.32731556X-RAY DIFFRACTION99.71
2.86-2.910.37561670.30531492X-RAY DIFFRACTION99.58
2.91-2.960.37691700.31861521X-RAY DIFFRACTION98.95
2.96-3.020.38581690.32261516X-RAY DIFFRACTION99.29
3.02-3.080.39431690.32661523X-RAY DIFFRACTION99.18
3.08-3.150.3951690.33451518X-RAY DIFFRACTION99.53
3.15-3.220.39021670.31111500X-RAY DIFFRACTION99.76
3.22-3.30.34341710.30131539X-RAY DIFFRACTION99.59
3.3-3.390.29911690.28351511X-RAY DIFFRACTION99.64
3.39-3.490.35261710.2691539X-RAY DIFFRACTION99.19
3.49-3.610.32231680.25481518X-RAY DIFFRACTION99.59
3.61-3.730.31271700.26211529X-RAY DIFFRACTION99.88
3.73-3.880.31221720.25141555X-RAY DIFFRACTION99.42
3.88-4.060.30951690.23931524X-RAY DIFFRACTION99.65
4.06-4.270.28731700.21971527X-RAY DIFFRACTION99.76
4.27-4.540.24221720.20531547X-RAY DIFFRACTION99.94
4.54-4.890.27771710.19561536X-RAY DIFFRACTION99.65
4.89-5.380.28011730.21931558X-RAY DIFFRACTION99.83
5.39-6.160.26721710.24031545X-RAY DIFFRACTION99.83
6.16-7.760.29161740.23621566X-RAY DIFFRACTION99.15
7.76-48.750.1911790.1791598X-RAY DIFFRACTION98.61

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