[English] 日本語
Yorodumi
- PDB-9ftu: Serial microseconds crystallography at ID29 using ASU extruder: T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ftu
TitleSerial microseconds crystallography at ID29 using ASU extruder: Thaumatin
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Serial Crystallography / serial microsecond crystallography / room temperature / ID29 / ESRF-EBS
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOrlans, J. / Rose, S.L. / Basu, S. / de Sanctis, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Chem / Year: 2025
Title: Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron.
Authors: Orlans, J. / Rose, S.L. / Ferguson, G. / Oscarsson, M. / Homs Puron, A. / Beteva, A. / Debionne, S. / Theveneau, P. / Coquelle, N. / Kieffer, J. / Busca, P. / Sinoir, J. / Armijo, V. / Lopez ...Authors: Orlans, J. / Rose, S.L. / Ferguson, G. / Oscarsson, M. / Homs Puron, A. / Beteva, A. / Debionne, S. / Theveneau, P. / Coquelle, N. / Kieffer, J. / Busca, P. / Sinoir, J. / Armijo, V. / Lopez Marrero, M. / Felisaz, F. / Papp, G. / Gonzalez, H. / Caserotto, H. / Dobias, F. / Gigmes, J. / Lebon, G. / Basu, S. / de Sanctis, D.
History
DepositionJun 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thaumatin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3782
Polymers22,2281
Non-polymers1501
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.550, 58.550, 151.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

-
Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 22228.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.8 M Sodium Potassium Tartrate

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Apr 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.75→54.56 Å / Num. obs: 27591 / % possible obs: 100 % / Redundancy: 1420 % / Biso Wilson estimate: 21.32 Å2 / CC star: 0.99 / R split: 0.0514 / Net I/σ(I): 18.82
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 1349 / CC star: 0.91 / R split: 0.528 / % possible all: 100
Serial crystallography sample deliveryDescription: ASU extruder / Method: injection

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.32 Å / SU ML: 0.1674 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.3238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1662 1999 7.27 %
Rwork0.1383 25505 -
obs0.1403 27504 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.55 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 10 192 1720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01341591
X-RAY DIFFRACTIONf_angle_d1.23382172
X-RAY DIFFRACTIONf_chiral_restr0.0886238
X-RAY DIFFRACTIONf_plane_restr0.0116289
X-RAY DIFFRACTIONf_dihedral_angle_d15.0097563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.28131400.24691781X-RAY DIFFRACTION100
1.79-1.840.2221400.18921790X-RAY DIFFRACTION100
1.84-1.90.2041390.16131784X-RAY DIFFRACTION100
1.9-1.960.18541400.1521778X-RAY DIFFRACTION100
1.96-2.030.19811400.16111786X-RAY DIFFRACTION100
2.03-2.110.18651410.14241802X-RAY DIFFRACTION100
2.11-2.20.20761400.14031780X-RAY DIFFRACTION100
2.2-2.320.17371430.13951813X-RAY DIFFRACTION100
2.32-2.470.14961410.13851816X-RAY DIFFRACTION100
2.47-2.660.16621430.15311815X-RAY DIFFRACTION100
2.66-2.920.16121430.1551827X-RAY DIFFRACTION100
2.92-3.350.18191440.14221840X-RAY DIFFRACTION100
3.35-4.220.1381480.11471890X-RAY DIFFRACTION99.9
4.22-46.320.1351570.11242003X-RAY DIFFRACTION99.91

+
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