[English] 日本語
Yorodumi
- PDB-7at6: Structure of thaumatin collected by femtosecond serial crystallog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7at6
TitleStructure of thaumatin collected by femtosecond serial crystallography on a COC membrane
ComponentsThaumatin I
KeywordsPLANT PROTEIN
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
R-1,2-PROPANEDIOL / L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsMartiel, I. / Marsh, M. / Vera, L. / Huang, C.Y. / Olieric, V. / Leonarski, P. / Nass, K. / Padeste, C. / Karpik, A. / Wang, M. / Pedrini, B.
CitationJournal: To Be Published
Title: Commissioning results from the SwissMX instrument for fixed target macromolecular crystallography at SwissFEL
Authors: Martiel, I. / Pradervand, C. / Panepucci, E. / Zamofing, T. / Nass, K. / Marsh, M. / Vera, L. / Hunag, C.Y. / Olieric, V. / Buntschu, D. / Kaelin, R. / Leonarski, P. / Ozerov, D. / Padeste, ...Authors: Martiel, I. / Pradervand, C. / Panepucci, E. / Zamofing, T. / Nass, K. / Marsh, M. / Vera, L. / Hunag, C.Y. / Olieric, V. / Buntschu, D. / Kaelin, R. / Leonarski, P. / Ozerov, D. / Padeste, C. / Karpik, A. / Thominet, V. / Hora, J. / Olieric, N. / Weinert, T. / Wranik, M. / Brunle, S. / Standfuss, J. / Aurelius, O. / John, J. / Hogbom, M. / Zhang, L. / Einsle, O. / Papp, G. / Basu, S. / Cipriani, F. / Beaud, P. / Mankowsky, R. / Glettig, W. / Mozzanica, A. / Redford, S. / Schmidt, B. / Bunk, O. / Abela, R. / Wang, M. / Lemke, H. / Pedrini, B.
History
DepositionOct 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: 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 13, 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 I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,94812
Polymers22,2281
Non-polymers72011
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-32 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.600, 58.600, 151.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 22228.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02883
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 1.6 M potassium sodium tartrate tetrahydrate 100mM Na Hepes pH 7.0 buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESB / Wavelength: 1.368 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.368 Å / Relative weight: 1
ReflectionResolution: 1.46→36.353 Å / Num. obs: 46820 / % possible obs: 100 % / Redundancy: 530 % / CC1/2: 0.992 / Net I/σ(I): 9.5
Reflection shellResolution: 1.46→1.49 Å / Num. unique obs: 4574 / CC1/2: 0.306
Serial crystallography measurementPulse photon energy: 9.06 keV
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: SwissMX CM / Sample dehydration prevention: cryogenic conditions / Sample holding: COC membrane / Support base: SwissMX goniometer
Serial crystallography data reductionFrames indexed: 31000 / XFEL pulse events: 174400

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AXR

4axr


Resolution: 1.46→36.353 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1766 2000 4.27 %
Rwork0.1585 44813 -
obs0.1593 46813 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.12 Å2 / Biso mean: 37.0631 Å2 / Biso min: 26.62 Å2
Refinement stepCycle: final / Resolution: 1.46→36.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 45 222 1792
Biso mean--57.46 47.84 -
Num. residues----206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.46-1.49650.3551390.33433129
1.4965-1.5370.30431410.30223147
1.537-1.58220.2791400.31163140
1.5822-1.63330.28351400.24763142
1.6333-1.69170.19331420.17473157
1.6917-1.75940.20251400.18693148
1.7594-1.83950.1771420.16873184
1.8395-1.93640.17751410.14913158
1.9364-2.05770.14511410.14123175
2.0577-2.21660.18941430.14733197
2.2166-2.43960.1821450.15673242
2.4396-2.79250.16381440.16363228
2.7925-3.51780.1921470.15743288
3.5178-36.3530.15721550.14833478
Refinement TLS params.Method: refined / Origin x: 12.35 Å / Origin y: 24.089 Å / Origin z: 32.606 Å
111213212223313233
T0.302 Å20.0067 Å2-0.0136 Å2-0.3184 Å20.0023 Å2--0.3252 Å2
L0.4432 °2-0.1116 °2-0.2337 °2-0.7013 °20.4233 °2--1.3582 °2
S0.0026 Å °0.0092 Å °-0.0214 Å °0.0299 Å °0.0127 Å °-0.009 Å °0.0259 Å °0.0695 Å °-0.0111 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:206 OR RESID 303:306 OR RESID 301:302 OR RESID 401:622 OR RESID 307:311 ) )A1 - 206
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:206 OR RESID 303:306 OR RESID 301:302 OR RESID 401:622 OR RESID 307:311 ) )A303 - 306
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:206 OR RESID 303:306 OR RESID 301:302 OR RESID 401:622 OR RESID 307:311 ) )A301 - 302
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:206 OR RESID 303:306 OR RESID 301:302 OR RESID 401:622 OR RESID 307:311 ) )A401 - 622
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:206 OR RESID 303:306 OR RESID 301:302 OR RESID 401:622 OR RESID 307:311 ) )A307 - 311

+
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