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

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Basic information

Entry
Database: PDB / ID: 6fqy
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) / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name
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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)107,7236
Polymers106,1122
Non-polymers1,6114
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12580 Å2
ΔGint-68 kcal/mol
Surface area35570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.320, 99.320, 181.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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 / Gene: PF14_0520, PF3D7_1454700 / Production host: Escherichia coli M15 (bacteria)
References: UniProt: Q8IKT2, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 25% MME550 and 0.1 M Hepes (4.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9538 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9538 Å / Relative weight: 1
ReflectionResolution: 2.9→43.6 Å / Num. obs: 23632 / % possible obs: 99.76 % / Redundancy: 5 % / Biso Wilson estimate: 74.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.085 / Rrim(I) all: 0.19 / Net I/σ(I): 9.69
Reflection shellResolution: 2.9→3 Å / Redundancy: 5 % / Num. unique obs: 2323 / CC1/2: 0.31 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2645: ???)refinement
XDS2017data reduction
XSCALE2017data scaling
PHENIXdev_2645: ???phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FQZ

6fqz


Resolution: 2.9→43.6 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.41
RfactorNum. reflection% reflection
Rfree0.2894 1876 7.94 %
Rwork0.2287 --
obs0.2334 23619 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7430 0 70 32 7532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057635
X-RAY DIFFRACTIONf_angle_d0.99410310
X-RAY DIFFRACTIONf_dihedral_angle_d5.2214596
X-RAY DIFFRACTIONf_chiral_restr0.0561135
X-RAY DIFFRACTIONf_plane_restr0.0041309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.97850.33661340.27681647X-RAY DIFFRACTION100
2.9785-3.06620.35191450.29631633X-RAY DIFFRACTION100
3.0662-3.16510.40681430.32231657X-RAY DIFFRACTION100
3.1651-3.27820.39391430.29931626X-RAY DIFFRACTION100
3.2782-3.40940.36591460.27621667X-RAY DIFFRACTION100
3.4094-3.56450.3291430.25211651X-RAY DIFFRACTION100
3.5645-3.75240.3051490.23321645X-RAY DIFFRACTION100
3.7524-3.98740.3041430.21271671X-RAY DIFFRACTION100
3.9874-4.29510.30471410.20041665X-RAY DIFFRACTION100
4.2951-4.7270.24281440.19271690X-RAY DIFFRACTION100
4.727-5.41020.24441460.21151669X-RAY DIFFRACTION100
5.4102-6.81310.31481450.26061715X-RAY DIFFRACTION100
6.8131-47.91050.2261540.19981807X-RAY DIFFRACTION100

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