[English] 日本語
Yorodumi
- PDB-7p23: Thaumatin-like protein of Puccinia graminis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p23
TitleThaumatin-like protein of Puccinia graminis
ComponentsThaumatin-like protein of Puccinia graminis
KeywordsUNKNOWN FUNCTION / Thaumatin-like protein
Function / homologyThaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / defense response / Thaumatin-like protein 1
Function and homology information
Biological speciesPuccinia graminis f. sp. tritici (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEder, M. / Hofer, G. / Odabas, M. / Keller, W.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundF 4604-B19 Austria
CitationJournal: To Be Published
Title: The structure of Thaumatin-like proteins of a bacterial, a fungal and an animal origin
Authors: Eder, M. / Hofer, G. / Odabas, M. / Keller, W.
History
DepositionJul 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Thaumatin-like protein of Puccinia graminis
B: Thaumatin-like protein of Puccinia graminis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0333
Polymers52,0102
Non-polymers231
Water11,259625
1
A: Thaumatin-like protein of Puccinia graminis


Theoretical massNumber of molelcules
Total (without water)26,0051
Polymers26,0051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thaumatin-like protein of Puccinia graminis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0282
Polymers26,0051
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.140, 77.523, 143.896
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Thaumatin-like protein of Puccinia graminis


Mass: 26004.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Puccinia graminis f. sp. tritici (strain CRL 75-36-700-3 / race SCCL) (fungus)
Strain: CRL 75-36-700-3 / race SCCL / Gene: PGTG_18309 / Plasmid: pPpT4-alpha / Production host: Komagataella pastoris (fungus) / Strain (production host): CBS7435 / References: UniProt: E3L7F9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.5
Details: PACT premier F12 (0.2 M Sodium nitrate, 0.1 M Bis-Tris propane pH 6.5, and 20 % w/v PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→42.2 Å / Num. obs: 79992 / % possible obs: 99.96 % / Redundancy: 12.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1396 / Rpim(I) all: 0.04067 / Rrim(I) all: 0.1456 / Net I/σ(I): 10.34
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.298 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 7882 / CC1/2: 0.703 / Rpim(I) all: 0.3669 / % possible all: 99.84

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ahn

2ahn


Resolution: 1.5→42.2 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 1099 1.37 %
Rwork0.1434 78920 -
obs0.144 79992 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.13 Å2 / Biso mean: 26.2133 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 1.5→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 1 625 4162
Biso mean--46.52 41.66 -
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.570.23821340.20189709984399
1.57-1.650.24821360.158197369872100
1.65-1.750.19211360.135497679903100
1.75-1.890.2071360.131497649900100
1.89-2.080.18971370.122498229959100
2.08-2.380.17341370.131398539990100
2.38-30.18671390.1578997510114100
3-42.20.18191440.14291029410438100

+
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