[English] 日本語
Yorodumi
- PDB-4zxr: Structure of Thaumatin wrapped in graphene within vacuum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zxr
TitleStructure of Thaumatin wrapped in graphene within vacuum
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / Thaumatin / vacuum / graphene / graphene-wrapped protein crystals
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: 1.92 Å
AuthorsAller, P. / Warren, A.J. / Trincao, J. / Evans, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: In vacuo X-ray data collection from graphene-wrapped protein crystals.
Authors: Warren, A.J. / Crawshaw, A.D. / Trincao, J. / Aller, P. / Alcock, S. / Nistea, I. / Salgado, P.S. / Evans, G.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5614
Polymers22,2271
Non-polymers3343
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint0 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.079, 59.079, 151.220
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: 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: Commercial thaumatin from Thaumatococcus danielli (Sigma-Aldrich) was resuspended in Milli-Q water to a concentration of 40 mg/mL. Sitting drops were made by mixing 4 uL of protein solution ...Details: Commercial thaumatin from Thaumatococcus danielli (Sigma-Aldrich) was resuspended in Milli-Q water to a concentration of 40 mg/mL. Sitting drops were made by mixing 4 uL of protein solution and 2 uL of reservoir solution [50 mM N-(2-Acetamido)iminodiacetic acid(ADA) pH 6.8, 600 mM potassium sodium tartrate and 20 % (v/v) Glycerol] and equilibrated against 500 uL of reservoir solution at 293K.

-
Data collection

DiffractionMean temperature: 295 K
Ambient temp details: sample wrapped in graphene whithin low vacuum in vacuum chamber
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2014
RadiationMonochromator: double crystals Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→41.78 Å / Num. obs: 20125 / % possible obs: 95.9 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.034 / Net I/σ(I): 10.6 / Num. measured all: 73107 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.92-1.973.60.582498613900.7450.34198.8
9.01-41.783.40.0329.67122080.9990.01883.6

-
Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KWN

1kwn
PDB Unreleased entry


Resolution: 1.92→41.78 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1713 / WRfactor Rwork: 0.145 / FOM work R set: 0.8698 / SU B: 5.934 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1048 / SU Rfree: 0.1017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1748 982 4.9 %RANDOM
Rwork0.1462 ---
obs0.1476 19143 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.69 Å2 / Biso mean: 37.326 Å2 / Biso min: 21.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1.92→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 22 87 1621
Biso mean--46.79 49.32 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021593
X-RAY DIFFRACTIONr_bond_other_d0.0020.021380
X-RAY DIFFRACTIONr_angle_refined_deg2.1821.9532178
X-RAY DIFFRACTIONr_angle_other_deg1.15533186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9965211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.53523.43864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31915216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.371510
X-RAY DIFFRACTIONr_chiral_restr0.3990.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
X-RAY DIFFRACTIONr_mcbond_it2.0532.606833
X-RAY DIFFRACTIONr_mcbond_other2.0492.601832
X-RAY DIFFRACTIONr_mcangle_it3.0893.8951041
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 57 -
Rwork0.25 1468 -
all-1525 -
obs--98.32 %
Refinement TLS params.Method: refined / Origin x: 12.2885 Å / Origin y: 24.8265 Å / Origin z: 32.6369 Å
111213212223313233
T0.0345 Å20.0055 Å2-0.0186 Å2-0.0077 Å2-0.0006 Å2--0.0452 Å2
L0.8769 °20.1027 °2-0.0784 °2-1.5799 °21.3525 °2--3.5922 °2
S0.0554 Å °-0.0182 Å °-0.1205 Å °0.0958 Å °-0.0395 Å °-0.0282 Å °0.3068 Å °0.0373 Å °-0.0159 Å °

+
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