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- PDB-6fqz: Plasmodium falciparum 6-phosphogluconate dehydrogenase in its apo... -

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Basic information

Entry
Database: PDB / ID: 6fqz
TitlePlasmodium falciparum 6-phosphogluconate dehydrogenase in its apo form, in complex with its cofactor NADP+ and in complex with its substrate 6-phosphogluconate
Components6-phosphogluconate dehydrogenase, decarboxylating
KeywordsOXIDOREDUCTASE / Plasmodium / complex / substrate / redox regulation
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / D-gluconate metabolic process / pentose-phosphate shunt, oxidative branch / pentose-phosphate shunt / NADP binding / cytosol
Similarity search - Function
6-Phosphogluconate Dehydrogenase, domain 3 / 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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...6-Phosphogluconate Dehydrogenase, domain 3 / 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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-PHOSPHOGLUCONIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFritz-Wolf, K. / Haeussler, K. / Reichmann, M. / Rahlfs, S. / Becker, K.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationBE1540/23-2 Germany
Hessian Excellence ProgrammLoewe center Druid, B3 and E3 Germany
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Characterization of Plasmodium falciparum 6-Phosphogluconate Dehydrogenase as an Antimalarial Drug Target.
Authors: Haeussler, K. / Fritz-Wolf, K. / Reichmann, M. / Rahlfs, S. / Becker, K.
History
DepositionFeb 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)108,98828
Polymers106,1122
Non-polymers2,87726
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18560 Å2
ΔGint-84 kcal/mol
Surface area33520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.660, 99.660, 180.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein 6-phosphogluconate dehydrogenase, decarboxylating


Mass: 53055.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF14_0520, PF3D7_1454700 / Production host: Escherichia coli M15 (bacteria)
References: UniProt: Q8IKT2, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Sugar ChemComp-6PG / 6-PHOSPHOGLUCONIC ACID


Type: D-saccharide / Mass: 276.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O10P / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 297 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 6PG-Pf6PGD crystals were crystallized with 24% PEG 1500 and 20% glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49.41 Å / Num. obs: 82520 / % possible obs: 99.96 % / Redundancy: 10 % / Biso Wilson estimate: 38.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.053 / Rrim(I) all: 0.17 / Net I/σ(I): 10.28
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 0.68 / Num. unique obs: 8165 / CC1/2: 0.33 / Rpim(I) all: 0.99 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIX(dev_2645: ???)refinement
XDS2017data reduction
XSCALE2017data scaling
PHENIXsvn 7924phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FQX

6fqx


Resolution: 1.9→49.409 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.14
RfactorNum. reflection% reflection
Rfree0.2293 2009 2.44 %
Rwork0.1977 --
obs0.1984 82501 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7438 0 186 273 7897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027758
X-RAY DIFFRACTIONf_angle_d0.49710424
X-RAY DIFFRACTIONf_dihedral_angle_d3.0266503
X-RAY DIFFRACTIONf_chiral_restr0.041141
X-RAY DIFFRACTIONf_plane_restr0.0031317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.94760.38031410.3535691X-RAY DIFFRACTION100
1.9476-2.00020.36351420.32395678X-RAY DIFFRACTION100
2.0002-2.05910.32051420.29045668X-RAY DIFFRACTION100
2.0591-2.12560.3031430.27165718X-RAY DIFFRACTION100
2.1256-2.20150.2681400.2575665X-RAY DIFFRACTION100
2.2015-2.28970.26181400.2325701X-RAY DIFFRACTION100
2.2897-2.39390.29441400.2235719X-RAY DIFFRACTION100
2.3939-2.52010.27761430.21745699X-RAY DIFFRACTION100
2.5201-2.6780.23481440.20435732X-RAY DIFFRACTION100
2.678-2.88470.24751470.19985738X-RAY DIFFRACTION100
2.8847-3.1750.19831440.18955773X-RAY DIFFRACTION100
3.175-3.63430.21881420.18095799X-RAY DIFFRACTION100
3.6343-4.57830.20071460.16135836X-RAY DIFFRACTION100
4.5783-49.42540.20021550.18246075X-RAY DIFFRACTION100

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