[English] 日本語
Yorodumi
- PDB-8a9f: Thaumatin, 9-11 fs FEL pulses as determined by XTCAV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a9f
TitleThaumatin, 9-11 fs FEL pulses as determined by XTCAV
ComponentsThaumatin-1
KeywordsANTIFUNGAL PROTEIN / free electron laser / radiation damage / disulfide bond
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 / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 1.88 Å
AuthorsBarends, T. / Nass, K. / Gorel, A. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Microcrystallization paper
Authors: Gorel, A. / Nass, K. / Barends, T. / Schlichting, I.
History
DepositionJun 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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
AAA: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3772
Polymers22,2271
Non-polymers1501
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.250, 58.250, 150.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Thaumatin-1


Mass: 22227.059 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: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7
Details: 0.8 M NA, K TARTRATE, 0.1 M NA HEPES PH 7.0, BATCH MODE, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.338 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.338 Å / Relative weight: 1
ReflectionResolution: 1.88→23.12 Å / Num. obs: 21989 / % possible obs: 100 % / Redundancy: 1 % / CC1/2: 0.955 / CC star: 0.989 / R split: 0.219 / Net I/σ(I): 3.5
Reflection shellResolution: 1.88→1.93 Å / % possible obs: 100 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1053 / CC1/2: 0.426 / CC star: 0.773 / R split: 0.97
Serial crystallography sample deliveryMethod: injection

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5FGT

5fgt


Resolution: 1.88→22.67 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.765 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2038 1022 4.663 %
Rwork0.1727 20896 -
all0.174 --
obs-21918 90.939 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.826 Å2
Baniso -1Baniso -2Baniso -3
1-0.251 Å2-0 Å2-0 Å2
2--0.251 Å2-0 Å2
3----0.502 Å2
Refinement stepCycle: LAST / Resolution: 1.88→22.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 132 1692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131614
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171415
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6692197
X-RAY DIFFRACTIONr_angle_other_deg1.421.5853294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.125.394216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91121.05376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82515240
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg7.723153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5871512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_nbd_refined0.1960.2283
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21314
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2797
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2123
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.211
X-RAY DIFFRACTIONr_nbd_other0.2080.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.210
X-RAY DIFFRACTIONr_mcbond_it2.0092.357831
X-RAY DIFFRACTIONr_mcbond_other1.9322.353830
X-RAY DIFFRACTIONr_mcangle_it2.9593.5281038
X-RAY DIFFRACTIONr_mcangle_other2.9583.5341039
X-RAY DIFFRACTIONr_scbond_it3.3552.751783
X-RAY DIFFRACTIONr_scbond_other3.362.754780
X-RAY DIFFRACTIONr_scangle_it5.2093.9461157
X-RAY DIFFRACTIONr_scangle_other5.2113.9471156
X-RAY DIFFRACTIONr_lrange_it6.99428.1551792
X-RAY DIFFRACTIONr_lrange_other6.80627.871767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.926-1.9810.371740.2861549X-RAY DIFFRACTION100
1.981-2.0420.296780.2721501X-RAY DIFFRACTION100
2.042-2.1080.288660.2481469X-RAY DIFFRACTION100
2.108-2.1810.286740.2311423X-RAY DIFFRACTION100
2.181-2.2630.2650.2071383X-RAY DIFFRACTION100
2.263-2.3540.226590.2011331X-RAY DIFFRACTION100
2.354-2.4580.215660.1911264X-RAY DIFFRACTION99.9249
2.458-2.5770.226680.2011207X-RAY DIFFRACTION100
2.577-2.7140.215560.191170X-RAY DIFFRACTION100
2.714-2.8760.175490.1641115X-RAY DIFFRACTION100
2.876-3.0710.184520.1561066X-RAY DIFFRACTION100
3.071-3.3120.173480.156972X-RAY DIFFRACTION100
3.312-3.6210.219450.141925X-RAY DIFFRACTION100
3.621-4.0360.145380.132828X-RAY DIFFRACTION100
4.036-4.6370.129390.108758X-RAY DIFFRACTION100
4.637-5.6220.154330.121642X-RAY DIFFRACTION100
5.622-7.7240.163250.132538X-RAY DIFFRACTION100

+
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