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- PDB-8c79: Crystal structure of Leishmania donovani 6-Phosphogluconate Dehyd... -

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Basic information

Entry
Database: PDB / ID: 8c79
TitleCrystal structure of Leishmania donovani 6-Phosphogluconate Dehydrogenase complexed with NADPH
Components6-phosphogluconate dehydrogenase, decarboxylating
KeywordsOXIDOREDUCTASE / Leishmania donovani / Trypanosoma / pentose phosphate pathway / 6-phosphogluconate dehydrogenase / antioxidant defense / drug target
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / D-gluconate metabolic process / pentose-phosphate shunt / NADP binding
Similarity search - Function
6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 ...6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / PHOSPHATE ION / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFritz-Wolf, K. / Berneburg, I. / Rahlfs, S. / Becker, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
LOEWE Center DRUIDB3/E3 Germany
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structure of Leishmania donovani 6-Phosphogluconate Dehydrogenase and Inhibition by Phosphine Gold(I) Complexes: A Potential Approach to Leishmaniasis Treatment.
Authors: Berneburg, I. / Stumpf, M. / Velten, A.S. / Rahlfs, S. / Przyborski, J. / Becker, K. / Fritz-Wolf, K.
History
DepositionJan 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name ..._pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase, decarboxylating
B: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4176
Polymers103,7362
Non-polymers1,6814
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-107 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.870, 117.350, 128.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 478 or (resid 501...
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERGLNGLNAA1 - 4781 - 478
d_12NDPNDPNDPNDPAC501
d_13PO4PO4PO4PO4AD502
d_21SERSERGLNGLNBB1 - 4781 - 478
d_22NDPNDPNDPNDPBE501
d_23PO4PO4PO4PO4BF502

NCS oper: (Code: givenMatrix: (-0.852514206644, 0.463560220199, 0.241519046288), (0.460927679916, 0.448792557048, 0.7655918721), (0.246505986454, 0.764000761117, -0.596269767517)Vector: -21. ...NCS oper: (Code: given
Matrix: (-0.852514206644, 0.463560220199, 0.241519046288), (0.460927679916, 0.448792557048, 0.7655918721), (0.246505986454, 0.764000761117, -0.596269767517)
Vector: -21.4259578523, -2.85030748542, 18.2618164561)

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Components

#1: Protein 6-phosphogluconate dehydrogenase, decarboxylating


Mass: 51867.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: gnd / Production host: Escherichia coli (E. coli) / References: UniProt: Q18L02
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 3000, 40 mM magnesium formate

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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 EIGER2 XE 16M / Detector: PIXEL / Date: Jun 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→46.1 Å / Num. obs: 18692 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 128.97 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.9
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 1841 / CC1/2: 0.35

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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: 1pgj

1pgj


Resolution: 3.1→46.07 Å / SU ML: 0.6809 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.9315
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3172 1870 10.01 %
Rwork0.2618 16819 -
obs0.2672 18689 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 126.5 Å2
Refinement stepCycle: LAST / Resolution: 3.1→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7278 0 87 1 7366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217510
X-RAY DIFFRACTIONf_angle_d0.525510158
X-RAY DIFFRACTIONf_chiral_restr0.03831104
X-RAY DIFFRACTIONf_plane_restr0.00361323
X-RAY DIFFRACTIONf_dihedral_angle_d8.92791045
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.932471277095 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.45781410.42911260X-RAY DIFFRACTION99.86
3.18-3.280.46521420.36081284X-RAY DIFFRACTION99.79
3.28-3.380.37151400.35411261X-RAY DIFFRACTION99.93
3.38-3.50.39621420.35741276X-RAY DIFFRACTION99.79
3.5-3.640.40761440.3311294X-RAY DIFFRACTION99.72
3.64-3.810.34491410.29041271X-RAY DIFFRACTION99.93
3.81-4.010.30821430.27821282X-RAY DIFFRACTION100
4.01-4.260.32791430.26431292X-RAY DIFFRACTION99.79
4.26-4.590.32551430.24871289X-RAY DIFFRACTION100
4.59-5.050.28611450.25971305X-RAY DIFFRACTION99.66
5.05-5.780.31561450.26471300X-RAY DIFFRACTION99.59
5.78-7.280.31831480.28431333X-RAY DIFFRACTION99.4
7.28-46.070.28181530.2121372X-RAY DIFFRACTION97.76

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