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

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Basic information

Entry
Database: PDB / ID: 6fqx
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 / redoxregulation
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / D-gluconate metabolic process / phosphogluconate dehydrogenase (decarboxylating) activity / 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
2-(2-ETHOXYETHOXY)ETHANOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Revision 1.3Jan 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: 6-phosphogluconate dehydrogenase, decarboxylating
D: 6-phosphogluconate dehydrogenase, decarboxylating
E: 6-phosphogluconate dehydrogenase, decarboxylating
F: 6-phosphogluconate dehydrogenase, decarboxylating
G: 6-phosphogluconate dehydrogenase, decarboxylating
H: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,12634
Polymers424,4478
Non-polymers2,67926
Water1,76598
1
A: 6-phosphogluconate dehydrogenase, decarboxylating
B: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,28313
Polymers106,1122
Non-polymers1,17111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13530 Å2
ΔGint-62 kcal/mol
Surface area34600 Å2
MethodPISA
2
C: 6-phosphogluconate dehydrogenase, decarboxylating
D: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5366
Polymers106,1122
Non-polymers4244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-66 kcal/mol
Surface area35030 Å2
MethodPISA
3
E: 6-phosphogluconate dehydrogenase, decarboxylating
F: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,89110
Polymers106,1122
Non-polymers7798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13290 Å2
ΔGint-65 kcal/mol
Surface area34530 Å2
MethodPISA
4
G: 6-phosphogluconate dehydrogenase, decarboxylating
H: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4165
Polymers106,1122
Non-polymers3043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-74 kcal/mol
Surface area35100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.450, 134.450, 406.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
6-phosphogluconate dehydrogenase, decarboxylating


Mass: 53055.875 Da / Num. of mol.: 8
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)

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Non-polymers , 5 types, 124 molecules

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


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 4,000, 15% glycerol, 0.085 M NaCitrat (pH 5.6), and 0.17 M Ammonium acetate

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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: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→46.53 Å / Num. obs: 101295 / % possible obs: 99.62 % / Redundancy: 10.3 % / Biso Wilson estimate: 73.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1825 / Rpim(I) all: 0.06 / Rrim(I) all: 0.192 / Net I/σ(I): 12.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 0.89 / Num. unique obs: 9878 / CC1/2: 0.25 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(dev_2645: ???)refinement
XDS2017data reduction
XSCALE2017data scaling
PHENIX(dev_2645: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w90

2w90


Resolution: 2.8→46.528 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.27
RfactorNum. reflection% reflection
Rfree0.2419 2022 2 %
Rwork0.1877 --
obs0.1889 101183 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→46.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29720 0 176 99 29995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0130403
X-RAY DIFFRACTIONf_angle_d1.29640947
X-RAY DIFFRACTIONf_dihedral_angle_d7.9418398
X-RAY DIFFRACTIONf_chiral_restr0.0764504
X-RAY DIFFRACTIONf_plane_restr0.0085232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.43021370.34796819X-RAY DIFFRACTION96
2.87-2.94760.32541360.29727056X-RAY DIFFRACTION99
2.9476-3.03430.29611420.26977069X-RAY DIFFRACTION100
3.0343-3.13220.30441420.25587092X-RAY DIFFRACTION100
3.1322-3.24420.33661370.23977091X-RAY DIFFRACTION100
3.2442-3.3740.33641480.22967130X-RAY DIFFRACTION100
3.374-3.52750.2721430.21087129X-RAY DIFFRACTION100
3.5275-3.71340.27281420.20177072X-RAY DIFFRACTION100
3.7134-3.9460.31071450.18247135X-RAY DIFFRACTION100
3.946-4.25040.23691480.16677079X-RAY DIFFRACTION100
4.2504-4.67780.22171470.15317109X-RAY DIFFRACTION100
4.6778-5.35390.20331510.16067127X-RAY DIFFRACTION100
5.3539-6.7420.21091550.18477113X-RAY DIFFRACTION100
6.742-46.53420.16121490.14957140X-RAY DIFFRACTION100

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