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- PDB-7zht: Leishmania donovani Glucose 6-Phosphate Dehydrogenase apo form -

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Basic information

Entry
Database: PDB / ID: 7zht
TitleLeishmania donovani Glucose 6-Phosphate Dehydrogenase apo form
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
Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn
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
C: Glucose-6-phosphate 1-dehydrogenase
D: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,47816
Polymers253,6324
Non-polymers84712
Water46826
1
A: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,3189
Polymers126,8162
Non-polymers5027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glucose-6-phosphate 1-dehydrogenase
D: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,1607
Polymers126,8162
Non-polymers3445
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.690, 65.820, 189.220
Angle α, β, γ (deg.)90.000, 92.350, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1
d_3ens_1
d_4ens_1

NCS oper:
IDCodeMatrixVector
1given(0.0736212433082, 0.514899847322, 0.854083169112), (0.507863101495, -0.756399293866, 0.412231947305), (0.858286072748, 0.403408298709, -0.317185689872)34.7957180855, -34.6583315331, -23.0606087518
2given(-0.128825839938, -0.495369691964, -0.859076696953), (0.441694824912, -0.804282032001, 0.397537538662), (-0.887867999542, -0.328236623922, 0.322414537678)140.041539786, 5.51614359068, 116.47936283
3given(-0.988690225594, 0.100336791298, 0.111463743556), (0.0990880360552, 0.994938508194, -0.016701078486), (-0.112575303358, -0.00546746961565, -0.993628153712)164.437482317, 26.8458698993, 100.957751344

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Components

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


Mass: 63407.887 Da / Num. of mol.: 4
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+)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 18 % PEG 3000, 200 mM ammonium chloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.8→39.2 Å / Num. obs: 70723 / % possible obs: 98.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 73.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 70723 / 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: 5UKW

5ukw


Resolution: 2.8→39.2 Å / SU ML: 0.5248 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.304 7052 10.01 %
Rwork0.244 63429 -
obs0.2499 70481 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16027 0 51 26 16104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008716403
X-RAY DIFFRACTIONf_angle_d1.711222166
X-RAY DIFFRACTIONf_chiral_restr0.09532434
X-RAY DIFFRACTIONf_plane_restr0.01922884
X-RAY DIFFRACTIONf_dihedral_angle_d20.80576119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.47272220.45312004X-RAY DIFFRACTION95.5
2.83-2.870.47952430.41652173X-RAY DIFFRACTION98.61
2.87-2.90.43622260.39912040X-RAY DIFFRACTION98.56
2.9-2.940.44082360.39142128X-RAY DIFFRACTION98.66
2.94-2.980.43532340.38572112X-RAY DIFFRACTION99.07
2.98-3.020.45212330.36992110X-RAY DIFFRACTION98.82
3.02-3.060.43822330.36582089X-RAY DIFFRACTION98.39
3.06-3.110.38482380.34342136X-RAY DIFFRACTION98.71
3.11-3.160.39422340.34032108X-RAY DIFFRACTION98.86
3.16-3.210.4292320.33732106X-RAY DIFFRACTION98.48
3.21-3.260.38492340.31842108X-RAY DIFFRACTION98.44
3.26-3.320.37812340.3092103X-RAY DIFFRACTION98.52
3.32-3.390.35032340.30052091X-RAY DIFFRACTION97.85
3.39-3.460.35642410.28152169X-RAY DIFFRACTION98.53
3.46-3.530.35552280.28562052X-RAY DIFFRACTION98.53
3.53-3.610.36942330.2812105X-RAY DIFFRACTION98.24
3.61-3.70.36762370.26762130X-RAY DIFFRACTION98.46
3.7-3.80.30722360.25512107X-RAY DIFFRACTION98.12
3.8-3.920.33082350.24462111X-RAY DIFFRACTION98.32
3.92-4.040.26882350.23432105X-RAY DIFFRACTION98.28
4.04-4.190.30242360.23022122X-RAY DIFFRACTION98.29
4.19-4.350.28112380.21462144X-RAY DIFFRACTION98.55
4.35-4.550.27022330.1962095X-RAY DIFFRACTION98.27
4.55-4.790.24312380.18692142X-RAY DIFFRACTION98.84
4.79-5.090.27622370.19382138X-RAY DIFFRACTION98.34
5.09-5.480.24532370.20962132X-RAY DIFFRACTION97.81
5.48-6.030.30272340.23282101X-RAY DIFFRACTION96.73
6.03-6.90.25692370.23022128X-RAY DIFFRACTION97.61
6.9-8.680.26352370.19572137X-RAY DIFFRACTION96.98
8.68-39.20.2222470.1812203X-RAY DIFFRACTION95.67

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