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

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Basic information

Entry
Database: PDB / ID: 7zhv
TitleLeishmania donovani Glucose 6-Phosphate Dehydrogenase complexed with 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 / 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 1.3Nov 20, 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

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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)127,1724
Polymers126,8162
Non-polymers3562
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-51 kcal/mol
Surface area46680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.740, 67.820, 120.750
Angle α, β, γ (deg.)90.000, 121.673, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 10 through 31 or resid 37 through 51 or resid 63 through 552))
d_2ens_1(chain "B" and (resid 10 through 471 or resid 482 through 552))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNARGA1 - 22
d_12ens_1PHEARGA28 - 42
d_13ens_1VALLYSA54 - 533
d_21ens_1GLNTHRB3 - 448
d_22ens_1ASPLYSB452 - 522

NCS oper: (Code: givenMatrix: (0.705178802526, 0.560104524289, -0.434747948055), (0.560917998042, -0.815752048838, -0.141136792829), (-0.433697885561, -0.144331274116, -0.889423761416)Vector: 50. ...NCS oper: (Code: given
Matrix: (0.705178802526, 0.560104524289, -0.434747948055), (0.560917998042, -0.815752048838, -0.141136792829), (-0.433697885561, -0.144331274116, -0.889423761416)
Vector: 50.8966447655, -91.8340635558, 98.3063536358)

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Components

#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+)
#2: 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 3.01 Å3/Da / Density % sol: 59.07 %
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: 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: 3.3→39.1 Å / Num. obs: 22384 / % possible obs: 96.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 128.55 Å2 / CC1/2: 1 / Net I/σ(I): 8.3
Reflection shellResolution: 3.3→3.4 Å / Num. unique obs: 2211 / CC1/2: 0.6

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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→39.1 Å / SU ML: 0.749 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.1011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.309 2219 9.97 %
Rwork0.2504 20041 -
obs0.2562 22260 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 138.85 Å2
Refinement stepCycle: LAST / Resolution: 3.3→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8342 0 21 4 8367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00998529
X-RAY DIFFRACTIONf_angle_d1.187411531
X-RAY DIFFRACTIONf_chiral_restr0.07111274
X-RAY DIFFRACTIONf_plane_restr0.01091501
X-RAY DIFFRACTIONf_dihedral_angle_d4.73081142
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 7.87214556656 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.370.64321400.64791258X-RAY DIFFRACTION97.22
3.37-3.450.57441340.49821228X-RAY DIFFRACTION96.39
3.45-3.540.4611380.41641231X-RAY DIFFRACTION96.89
3.54-3.630.42351370.34071238X-RAY DIFFRACTION96.83
3.63-3.740.35811370.33111244X-RAY DIFFRACTION97.39
3.74-3.860.36921390.29221243X-RAY DIFFRACTION97.53
3.86-40.36561390.29811254X-RAY DIFFRACTION97.01
4-4.160.35821380.28631264X-RAY DIFFRACTION97.77
4.16-4.350.33571360.25661244X-RAY DIFFRACTION96.44
4.35-4.570.33291390.23111250X-RAY DIFFRACTION96.73
4.58-4.860.27521410.21811271X-RAY DIFFRACTION97.65
4.86-5.240.25811410.23291269X-RAY DIFFRACTION97.92
5.24-5.760.3141410.23851262X-RAY DIFFRACTION97.57
5.76-6.590.30121380.24821258X-RAY DIFFRACTION96.21
6.59-8.30.2741410.22751260X-RAY DIFFRACTION96.02
8.3-39.10.23181400.1811267X-RAY DIFFRACTION92.99

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