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- PDB-7zhw: Leishmania donovani Glucose 6-Phosphate Dehydrogenase complexed w... -

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Basic information

Entry
Database: PDB / ID: 7zhw
TitleLeishmania donovani Glucose 6-Phosphate Dehydrogenase complexed with NADP(H) and Glucose 6-Phosphate
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: 3.3 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)129,32914
Polymers126,8162
Non-polymers2,51412
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-121 kcal/mol
Surface area47060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.830, 66.770, 121.020
Angle α, β, γ (deg.)90.000, 120.708, 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: 63407.887 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+)
#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, 12 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 12 % PEG 3000 and 200 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: 3.3→49.3 Å / Num. obs: 22716 / % possible obs: 99.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 124.7 Å2 / CC1/2: 1 / Net I/σ(I): 9.7
Reflection shellResolution: 3.3→3.4 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 11462 / CC1/2: 0.7 / % possible all: 98.6

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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: 3.3→49.3 Å / SU ML: 0.6118 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.4726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2625 2246 10.01 %
Rwork0.2359 20189 -
obs0.2386 22435 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 144.88 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8457 0 145 1 8603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00248772
X-RAY DIFFRACTIONf_angle_d0.614811878
X-RAY DIFFRACTIONf_chiral_restr0.04311307
X-RAY DIFFRACTIONf_plane_restr0.00361527
X-RAY DIFFRACTIONf_dihedral_angle_d6.40981179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.370.52981400.45491243X-RAY DIFFRACTION98.86
3.37-3.450.46631340.42091201X-RAY DIFFRACTION97.8
3.45-3.540.41341400.36071269X-RAY DIFFRACTION98.46
3.54-3.630.39711360.3371213X-RAY DIFFRACTION98.68
3.63-3.740.37941410.32221272X-RAY DIFFRACTION98.88
3.74-3.860.33671380.31238X-RAY DIFFRACTION98.78
3.86-40.3631360.29881243X-RAY DIFFRACTION98.29
4-4.160.28361410.27041255X-RAY DIFFRACTION99.15
4.16-4.350.26481400.23061262X-RAY DIFFRACTION99.08
4.35-4.580.26061410.21671263X-RAY DIFFRACTION99.79
4.58-4.860.23091400.20451256X-RAY DIFFRACTION99.64
4.86-5.240.29241420.23641281X-RAY DIFFRACTION99.93
5.24-5.760.26291410.23771276X-RAY DIFFRACTION99.79
5.76-6.60.27011450.24921296X-RAY DIFFRACTION99.86
6.6-8.30.25621430.24011287X-RAY DIFFRACTION99.65
8.3-49.30.17411480.16551334X-RAY DIFFRACTION99.53

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