[English] 日本語
Yorodumi
- PDB-4ekt: Final Thaumatin Structure for Radiation Damage Experiment at 180 K -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ekt
TitleFinal Thaumatin Structure for Radiation Damage Experiment at 180 K
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / sweet protein / radiation damage
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
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
AuthorsWarkentin, M. / Badeau, R. / Hopkins, J.B. / Thorne, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Spatial distribution of radiation damage to crystalline proteins at 25-300 K.
Authors: Warkentin, M. / Badeau, R. / Hopkins, J.B. / Thorne, R.E.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3932
Polymers22,2431
Non-polymers1501
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.900, 57.900, 150.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Thaumatin-1 / Thaumatin I


Mass: 22243.119 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.: 238 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHAUMATIN WAS PURCHASED FROM SIGMA-ALDRICH (CATALOG # T7638) AND CONTAINED A MIXTURE OF THAUMATIN I ...THAUMATIN WAS PURCHASED FROM SIGMA-ALDRICH (CATALOG # T7638) AND CONTAINED A MIXTURE OF THAUMATIN I AND THAUMATIN II. LYS46 WAS USED IN PLACE OF ASN46 AND ASP113 WAS USED IN PLACE OF ASN113 AS WAS DONE IN ENTRY 1RQW AND AS SUGGESTED BY KO ET AL., ACTA CRYST. D50,813(1994).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: sodium potassium tartrate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 22, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 26070 / % possible obs: 97.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.088 / Χ2: 1.228 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.813.40.44724780.631195.3
1.81-1.8950.39525640.652199.1
1.89-1.975.90.29525991.111199.2
1.97-2.076.10.21226050.79199.1
2.07-2.26.10.15926020.889198.7
2.2-2.386.20.12925880.953198.4
2.38-2.616.20.10326170.963198.1
2.61-2.996.20.07926221.089197.6
2.99-3.776.10.06326341.437196.5
3.77-505.80.06627613.298194

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
BUSTER2.8.0phasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20.66 Å / Cor.coef. Fo:Fc: 0.9556 / Cor.coef. Fo:Fc free: 0.9349 / Occupancy max: 1 / Occupancy min: 0.11 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 1316 5.05 %RANDOM
Rwork0.1738 ---
obs0.1752 26034 --
Displacement parametersBiso max: 112.23 Å2 / Biso mean: 26.3867 Å2 / Biso min: 10.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.9207 Å20 Å20 Å2
2---1.9207 Å20 Å2
3---3.8414 Å2
Refine analyzeLuzzati coordinate error obs: 0.174 Å
Refinement stepCycle: LAST / Resolution: 1.75→20.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 10 238 1800
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d557SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes243HARMONIC5
X-RAY DIFFRACTIONt_it1664HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion225SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2063SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1664HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2265HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.26
X-RAY DIFFRACTIONt_other_torsion15.98
LS refinement shellResolution: 1.75→1.82 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.297 130 4.6 %
Rwork0.2208 2695 -
all0.2244 2825 -

+
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