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

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Basic information

Entry
Database: PDB / ID: 7zhu
TitleLeishmania donovani Glucose 6-Phosphate Dehydrogenase 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, oxidative branch / glucose metabolic process / NADP binding / cytosol
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: 1.7 Å
AuthorsFritz-Wolf, K. / Berneburg, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
LOEWE Center DRUID (Project B3 and E3) within the Hessian Excellence ProgramProject 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)131,31843
Polymers126,8162
Non-polymers4,50241
Water16,033890
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16350 Å2
ΔGint-42 kcal/mol
Surface area45850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.230, 65.650, 119.250
Angle α, β, γ (deg.)90.000, 120.533, 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: 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 (E. coli)
References: UniProt: A2CIL3, glucose-6-phosphate dehydrogenase (NADP+)

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Non-polymers , 6 types, 931 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.: 25 / 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.: 6 / 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.: 890 / 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: 2.97 Å3/Da / Density % sol: 58.55 %
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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→48.1 Å / Num. obs: 159924 / % possible obs: 97.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 33.94 Å2 / CC1/2: 1 / Net I/σ(I): 11.9
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 15809 / CC1/2: 0.4 / % possible all: 97.2

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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: 1.7→48.07 Å / SU ML: 0.3035 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6097
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 12776 8 %
Rwork0.1968 146912 -
obs0.1992 159688 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.22 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8535 0 283 890 9708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00659027
X-RAY DIFFRACTIONf_angle_d0.89912171
X-RAY DIFFRACTIONf_chiral_restr0.05361327
X-RAY DIFFRACTIONf_plane_restr0.00771560
X-RAY DIFFRACTIONf_dihedral_angle_d17.32023363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.44114170.41634799X-RAY DIFFRACTION96.31
1.72-1.740.41064240.39084856X-RAY DIFFRACTION97.74
1.74-1.760.39944210.37764843X-RAY DIFFRACTION97.59
1.76-1.780.38784240.36374843X-RAY DIFFRACTION97
1.78-1.810.46794190.43194850X-RAY DIFFRACTION97.29
1.81-1.830.46014240.44544861X-RAY DIFFRACTION97.78
1.83-1.860.43854210.40964857X-RAY DIFFRACTION97.34
1.86-1.890.41114240.34614863X-RAY DIFFRACTION97.55
1.89-1.920.32484250.30044868X-RAY DIFFRACTION97.84
1.92-1.950.30464230.2764896X-RAY DIFFRACTION97.88
1.95-1.980.29334240.25674863X-RAY DIFFRACTION98.03
1.98-2.020.27934260.24574894X-RAY DIFFRACTION98.35
2.02-2.060.26914280.23964913X-RAY DIFFRACTION98.14
2.06-2.10.26764270.23664908X-RAY DIFFRACTION98.49
2.1-2.140.28294240.23584887X-RAY DIFFRACTION98.39
2.14-2.190.26844320.23824965X-RAY DIFFRACTION98.29
2.19-2.250.27894240.21394880X-RAY DIFFRACTION98.44
2.25-2.310.2424260.20464909X-RAY DIFFRACTION98.5
2.31-2.380.22954290.19714930X-RAY DIFFRACTION98.28
2.38-2.450.23884250.19544889X-RAY DIFFRACTION98.1
2.45-2.540.2274310.18984952X-RAY DIFFRACTION98.21
2.54-2.640.25634270.19124927X-RAY DIFFRACTION98.47
2.64-2.760.23024250.19144885X-RAY DIFFRACTION98.22
2.76-2.910.21764310.18244948X-RAY DIFFRACTION97.82
2.91-3.090.22444260.18434898X-RAY DIFFRACTION98.36
3.09-3.330.20734310.18134961X-RAY DIFFRACTION98.18
3.33-3.660.19914270.16814905X-RAY DIFFRACTION97.67
3.66-4.190.18864220.16014858X-RAY DIFFRACTION96.26
4.19-5.280.17264330.15294979X-RAY DIFFRACTION97.65
5.28-48.070.18534360.17575025X-RAY DIFFRACTION96.38

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