[English] 日本語
Yorodumi
- PDB-7v6g: Structure of Candida albicans Fructose-1,6-bisphosphate aldolase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v6g
TitleStructure of Candida albicans Fructose-1,6-bisphosphate aldolase mutation C157S with CN39
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / FBA
Function / homology
Function and homology information


symbiont-mediated perturbation of host immune response / hyphal cell wall / fungal-type cell wall / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / biological process involved in interaction with host / gluconeogenesis / glycolytic process / cell surface / zinc ion binding ...symbiont-mediated perturbation of host immune response / hyphal cell wall / fungal-type cell wall / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / biological process involved in interaction with host / gluconeogenesis / glycolytic process / cell surface / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase-type TIM barrel
Similarity search - Domain/homology
~{N}-(4-aminophenyl)-2-selanyl-benzamide / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.343 Å
AuthorsCao, H. / Huang, Y. / Chen, H. / Wan, C. / Ren, Y. / Wan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Guided Discovery of the Novel Covalent Allosteric Site and Covalent Inhibitors of Fructose-1,6-Bisphosphate Aldolase to Overcome the Azole Resistance of Candidiasis.
Authors: Wen, W. / Cao, H. / Huang, Y. / Tu, J. / Wan, C. / Wan, J. / Han, X. / Chen, H. / Liu, J. / Rao, L. / Su, C. / Peng, C. / Sheng, C. / Ren, Y.
History
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9908
Polymers80,1522
Non-polymers8376
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-101 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.182, 56.536, 82.034
Angle α, β, γ (deg.)90.000, 96.070, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Fructose-bisphosphate aldolase / FBP aldolase / FBPA / Fructose-1 / 6-bisphosphate aldolase


Mass: 40076.078 Da / Num. of mol.: 2 / Mutation: C157S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / Gene: FBA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9URB4, fructose-bisphosphate aldolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-6Y3 / ~{N}-(4-aminophenyl)-2-selanyl-benzamide / amino-ebselen (open form)


Mass: 291.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N2OSe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM Hepes pH =7.5, 11% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.343→39.821 Å / Num. obs: 30829 / % possible obs: 99.38 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 12.29
Reflection shellResolution: 2.343→2.427 Å / Num. unique obs: 3029 / CC1/2: 0.871

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNK

6lnk


Resolution: 2.343→39.821 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 1541 5 %
Rwork0.2038 29272 -
obs0.2065 30813 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.07 Å2 / Biso mean: 56.0309 Å2 / Biso min: 30.42 Å2
Refinement stepCycle: final / Resolution: 2.343→39.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5157 0 44 94 5295
Biso mean--60.97 52.63 -
Num. residues----673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3434-2.41910.29741370.2484259797
2.4191-2.50550.32141380.2501261499
2.5055-2.60580.36031400.2487265399
2.6058-2.72440.30411380.2436263099
2.7244-2.8680.3211380.2389264999
2.868-3.04760.28841400.23992652100
3.0476-3.28280.30151400.24782664100
3.2828-3.6130.28691400.23322663100
3.613-4.13530.23671420.18872687100
4.1353-5.20820.22531420.16652692100
5.2082-39.8210.20851460.17032771100

+
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