[English] 日本語
Yorodumi
- PDB-7p22: Thaumatin-like protein of Amycolatopsis rifamycinica -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p22
TitleThaumatin-like protein of Amycolatopsis rifamycinica
ComponentsThaumatin pathogenesis-like protein
KeywordsUNKNOWN FUNCTION / Thaumatin-like protein
Function / homologyThaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Thaumatin pathogenesis-like protein
Function and homology information
Biological speciesAmycolatopsis rifamycinica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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. / Keller, W. / Hofer, G. / Odabas, M.
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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thaumatin pathogenesis-like protein
B: Thaumatin pathogenesis-like protein


Theoretical massNumber of molelcules
Total (without water)52,1292
Polymers52,1292
Non-polymers00
Water6,846380
1
A: Thaumatin pathogenesis-like protein


Theoretical massNumber of molelcules
Total (without water)26,0651
Polymers26,0651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thaumatin pathogenesis-like protein


Theoretical massNumber of molelcules
Total (without water)26,0651
Polymers26,0651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.341, 80.341, 169.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Thaumatin pathogenesis-like protein


Mass: 26064.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis rifamycinica (bacteria) / Gene: DV20_29330 / Plasmid: pJC40 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express lysY / References: UniProt: A0A066TYR3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.5
Details: JCSG+ D1 condition (0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES pH 7.0 and 30 % v/v PEG 400)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.87→46.29 Å / Num. obs: 46839 / % possible obs: 99.92 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1317 / Rpim(I) all: 0.05489 / Rrim(I) all: 0.143 / Net I/σ(I): 11.35
Reflection shellResolution: 1.87→1.937 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.127 / Num. unique obs: 4587 / CC1/2: 0.648 / Rpim(I) all: 0.4667 / % possible all: 99.91

-
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: 1.87→46.29 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 2396 5.09 %
Rwork0.1815 44663 -
obs0.1828 46839 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.05 Å2 / Biso mean: 27.611 Å2 / Biso min: 14.88 Å2
Refinement stepCycle: final / Resolution: 1.87→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 0 380 3648
Biso mean---34.73 -
Num. residues----441
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.87-1.90.28011260.2665250797
1.9-1.940.26711240.24932585100
1.94-1.990.23921350.23252574100
1.99-2.040.25941430.22442605100
2.04-2.10.27981610.21122551100
2.1-2.160.21041270.19912611100
2.16-2.230.23671070.19652638100
2.23-2.310.23151330.19652601100
2.31-2.40.22941390.18572616100
2.4-2.510.24531380.18752620100
2.51-2.640.23331410.18282607100
2.64-2.80.21521500.19142626100
2.81-3.020.23341610.18762618100
3.02-3.330.21241360.17752663100
3.33-3.810.17651580.15732668100
3.81-4.80.13791460.15112713100
4.8-46.290.19941710.16952860100

+
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