[English] 日本語
Yorodumi
- PDB-6fqx: Plasmodium falciparum 6-phosphogluconate dehydrogenase in its apo... -

+
Open data


ID or keywords:

Loading...

-
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) / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more