[English] 日本語
Yorodumi
- PDB-5o9p: Crystal structure of Gas2 in complex with compound 10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o9p
TitleCrystal structure of Gas2 in complex with compound 10
Components1,3-beta-glucanosyltransferase GAS2
KeywordsTRANSFERASE / Aspergillus fumigatus / AfGel4 / ScGas2 / transglycosylases / glucanosyltransferases / cell wall remodeling / fungal cell wall
Function / homology
Function and homology information


1,3-beta-glucanosyltransferase activity / fungal-type cell wall (1->3)-beta-D-glucan biosynthetic process / ascospore wall assembly / fungal-type cell wall organization / fungal-type vacuole / Transferases; Glycosyltransferases; Hexosyltransferases / side of membrane / plasma membrane / cytoplasm
Similarity search - Function
Glucanosyltransferase / Glucanosyltransferase / X8 domain / X8 domain / Possibly involved in carbohydrate binding / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-9P8 / 1,3-beta-glucanosyltransferase GAS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDelso, I. / Valero-Gonzalez, J. / Gomollon-Bel, F. / Castro-Lopez, J. / Fang, W. / Navratilova, I. / Van Aalten, D. / Tejero, T. / Merino, P. / Hurtado-Guerrero, R.
CitationJournal: ChemMedChem / Year: 2018
Title: Inhibitors against Fungal Cell Wall Remodeling Enzymes.
Authors: Delso, I. / Valero-Gonzalez, J. / Gomollon-Bel, F. / Castro-Lopez, J. / Fang, W. / Navratilova, I. / van Aalten, D.M.F. / Tejero, T. / Merino, P. / Hurtado-Guerrero, R.
History
DepositionJun 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1,3-beta-glucanosyltransferase GAS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1653
Polymers62,4261
Non-polymers7392
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint3 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.067, 70.953, 150.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 1,3-beta-glucanosyltransferase GAS2 / Glycolipid-anchored surface protein 2


Mass: 62426.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: GAS2, YLR343W, L8300.5 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q06135, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-9P8 / (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-3,5-bis(oxidanyl)-6-[4-(pyridin-2-ylmethoxymethyl)-1,2,3-triazol-1-yl]oxan-4-yl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-oxane-3,4,5-triol


Mass: 676.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H40N4O16
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3500, ammonium sulfate, BIS-Tris pH 6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→75.5 Å / Num. obs: 54873 / % possible obs: 99.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 5.7
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W62

2w62


Resolution: 1.75→75.5 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.675 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24461 1542 2.8 %RANDOM
Rwork0.21069 ---
obs0.21166 53117 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.772 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2--1.67 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.75→75.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3463 0 51 262 3776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023651
X-RAY DIFFRACTIONr_bond_other_d0.0020.023292
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9934944
X-RAY DIFFRACTIONr_angle_other_deg1.0393.0127642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7924.74173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04315592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9281515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214040
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02817
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9921.8121735
X-RAY DIFFRACTIONr_mcbond_other0.9881.8111734
X-RAY DIFFRACTIONr_mcangle_it1.7252.72160
X-RAY DIFFRACTIONr_mcangle_other1.7252.7012161
X-RAY DIFFRACTIONr_scbond_it1.0181.871916
X-RAY DIFFRACTIONr_scbond_other1.0171.871916
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6912.7552785
X-RAY DIFFRACTIONr_long_range_B_refined3.55514.6084253
X-RAY DIFFRACTIONr_long_range_B_other3.55514.6124254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 116 -
Rwork0.248 3899 -
obs--99.5 %
Refinement TLS params.Method: refined / Origin x: 5.5198 Å / Origin y: 8.1923 Å / Origin z: -20.0594 Å
111213212223313233
T0.0373 Å2-0.0034 Å20.0051 Å2-0.1282 Å2-0.023 Å2--0.0628 Å2
L0.4905 °2-0.1112 °2-0.0953 °2-0.2384 °20.1089 °2--0.1359 °2
S0.0079 Å °0.0223 Å °-0.1061 Å °-0.0035 Å °0.0171 Å °-0.0102 Å °-0.0541 Å °0.014 Å °-0.025 Å °

+
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