[English] 日本語
Yorodumi
- PDB-8c79: Crystal structure of Leishmania donovani 6-Phosphogluconate Dehyd... -

+
Open data


ID or keywords:

Loading...

-
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


D-gluconate metabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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 / 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 / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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