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- PDB-7zhx: Leishmania donovani Glucose 6-Phosphate Dehydrogenase (N-terminal... -

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Basic information

Entry
Database: PDB / ID: 7zhx
TitleLeishmania donovani Glucose 6-Phosphate Dehydrogenase (N-terminal deletion variant)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
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
Chem-NDP / DI(HYDROXYETHYL)ETHER / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,31811
Polymers56,7941
Non-polymers1,52410
Water6,864381
1
A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,63622
Polymers113,5872
Non-polymers3,04920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area10880 Å2
ΔGint29 kcal/mol
Surface area38100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.750, 229.660, 83.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-759-

HOH

21A-882-

HOH

31A-899-

HOH

41A-939-

HOH

51A-1037-

HOH

61A-1078-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 56793.559 Da / Num. of mol.: 1
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 , 5 types, 391 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 3.2 Å3/Da / Density % sol: 61.55 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 6 % PEG 3000, 200 mM AmCl2

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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: Feb 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.3 Å / Num. obs: 58616 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 33.36 Å2 / CC1/2: 1 / Net I/σ(I): 18.9
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 32174 / CC1/2: 0.8

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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: 1.9→47.3 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2103 4692 8 %
Rwork0.182 53924 -
obs0.1843 58616 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.72 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3801 0 99 381 4281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874005
X-RAY DIFFRACTIONf_angle_d0.98225408
X-RAY DIFFRACTIONf_chiral_restr0.0597590
X-RAY DIFFRACTIONf_plane_restr0.0084694
X-RAY DIFFRACTIONf_dihedral_angle_d10.0402561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-20.44111530.37551753X-RAY DIFFRACTION99.01
1.91-1.930.38871530.3081763X-RAY DIFFRACTION99.38
1.93-1.960.28331560.26871782X-RAY DIFFRACTION99.18
1.96-1.980.26771530.2471771X-RAY DIFFRACTION99.9
1.98-2.010.29871530.25071758X-RAY DIFFRACTION99.74
2.01-2.030.24651560.26371789X-RAY DIFFRACTION99.79
2.03-2.060.34721550.28041783X-RAY DIFFRACTION99.49
2.06-2.090.32011550.2471776X-RAY DIFFRACTION99.48
2.09-2.130.2481560.20371787X-RAY DIFFRACTION99.59
2.13-2.160.26271550.19961788X-RAY DIFFRACTION99.64
2.16-2.20.25751540.19561765X-RAY DIFFRACTION99.79
2.2-2.240.25291550.20621788X-RAY DIFFRACTION99.59
2.24-2.280.24681540.20531771X-RAY DIFFRACTION99.48
2.28-2.330.24041560.18661784X-RAY DIFFRACTION99.74
2.33-2.380.25561550.19181781X-RAY DIFFRACTION99.85
2.38-2.440.20021550.1871789X-RAY DIFFRACTION99.79
2.44-2.50.23971560.18781788X-RAY DIFFRACTION99.59
2.5-2.560.23841560.18931792X-RAY DIFFRACTION99.95
2.56-2.640.21821580.18321817X-RAY DIFFRACTION99.9
2.64-2.720.19631540.17841781X-RAY DIFFRACTION99.9
2.72-2.820.21271570.17631802X-RAY DIFFRACTION99.59
2.82-2.930.1981570.17271802X-RAY DIFFRACTION99.59
2.93-3.070.1941560.18061800X-RAY DIFFRACTION100
3.07-3.230.20331590.18271820X-RAY DIFFRACTION100
3.23-3.430.22041580.18111815X-RAY DIFFRACTION100
3.43-3.70.19811570.17181816X-RAY DIFFRACTION99.8
3.7-4.070.21221590.15881823X-RAY DIFFRACTION99.65
4.07-4.660.15451600.14331844X-RAY DIFFRACTION99.75
4.66-5.870.17961610.16071853X-RAY DIFFRACTION99.31

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