[English] 日本語
Yorodumi
- PDB-8jz0: Crystal structure of a single-chain monellin mutant C41A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jz0
TitleCrystal structure of a single-chain monellin mutant C41A
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / Sweet protein
Function / homologyMonellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / Cystatin superfamily / Monellin chain A / Monellin chain B
Function and homology information
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.229 Å
AuthorsYasui, N. / Ohnuma, K. / Yamashita, A.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H02841 Japan
Japan Society for the Promotion of Science (JSPS)21K19084 Japan
CitationJournal: Protein J. / Year: 2023
Title: Investigating the Effect of Substituting a Single Cysteine Residue on the Thermal Stability of an Engineered Sweet Protein, Single-Chain Monellin.
Authors: Ohnuma, K. / Yamashita, A. / Yasui, N.
History
DepositionJul 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monellin chain B,Monellin chain A
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)22,3912
Polymers22,3912
Non-polymers00
Water3,351186
1
A: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,1961
Polymers11,1961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,1961
Polymers11,1961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.695, 39.748, 44.410
Angle α, β, γ (deg.)106.22, 109.25, 103.35
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Monellin chain B,Monellin chain A / Monellin chain II / Monellin chain I


Mass: 11195.691 Da / Num. of mol.: 2 / Mutation: C41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02882, UniProt: P02881
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate, pH 5.0, and 35% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.229→50 Å / Num. obs: 84210 / % possible obs: 78.5 % / Redundancy: 1.785 % / CC1/2: 0.995 / Net I/σ(I): 11.02
Reflection shellResolution: 1.23→1.3 Å / Num. unique obs: 5776 / CC1/2: 0.858

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOL

1mol


Resolution: 1.229→35.66 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 4263 5.06 %
Rwork0.2126 --
obs0.214 84196 78.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.229→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 0 186 1679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061541
X-RAY DIFFRACTIONf_angle_d0.9172077
X-RAY DIFFRACTIONf_dihedral_angle_d10.817599
X-RAY DIFFRACTIONf_chiral_restr0.039211
X-RAY DIFFRACTIONf_plane_restr0.005269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.229-1.24290.3806440.3311833X-RAY DIFFRACTION25
1.2429-1.25750.3798470.3352936X-RAY DIFFRACTION28
1.2575-1.27290.3488650.31821148X-RAY DIFFRACTION34
1.2729-1.2890.3566740.31631306X-RAY DIFFRACTION40
1.289-1.3060.3669650.30991543X-RAY DIFFRACTION44
1.306-1.32390.31431100.29871741X-RAY DIFFRACTION52
1.3239-1.34280.3478990.28692098X-RAY DIFFRACTION62
1.3428-1.36280.31091510.28832705X-RAY DIFFRACTION80
1.3628-1.38410.32761720.2892866X-RAY DIFFRACTION86
1.3841-1.40680.29051470.29532995X-RAY DIFFRACTION88
1.4068-1.43110.28581750.2833007X-RAY DIFFRACTION90
1.4311-1.45710.34511380.28253079X-RAY DIFFRACTION90
1.4571-1.48510.33251610.28273081X-RAY DIFFRACTION91
1.4851-1.51540.33541730.2633054X-RAY DIFFRACTION90
1.5154-1.54840.29951850.24933039X-RAY DIFFRACTION91
1.5484-1.58440.30291940.24533112X-RAY DIFFRACTION91
1.5844-1.6240.31561370.26233053X-RAY DIFFRACTION91
1.624-1.66790.26921700.23773154X-RAY DIFFRACTION92
1.6679-1.7170.25781450.23483114X-RAY DIFFRACTION92
1.717-1.77240.25081490.24113132X-RAY DIFFRACTION92
1.7724-1.83580.30431510.2423083X-RAY DIFFRACTION91
1.8358-1.90930.23561570.22483123X-RAY DIFFRACTION92
1.9093-1.99610.24731630.2163155X-RAY DIFFRACTION92
1.9961-2.10140.23931530.21123143X-RAY DIFFRACTION92
2.1014-2.2330.21671730.19623145X-RAY DIFFRACTION93
2.233-2.40540.25041750.19933080X-RAY DIFFRACTION92
2.4054-2.64740.22581620.20313186X-RAY DIFFRACTION93
2.6474-3.03030.23282190.19373096X-RAY DIFFRACTION94
3.0303-3.81720.19331550.17783109X-RAY DIFFRACTION92
3.8172-35.660.19211540.18632817X-RAY DIFFRACTION83

+
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