[English] 日本語
Yorodumi
- PDB-6i3a: Crystal structure of v22Pizza6-AYW, a circularly permuted designe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i3a
TitleCrystal structure of v22Pizza6-AYW, a circularly permuted designer protein
Componentsv22Pizza6-AYW
KeywordsDE NOVO PROTEIN / circularly permuted designer protein / artificial protein / beta-propeller / Pizza
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta / BROMIDE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMylemans, B. / Noguchi, H. / Deridder, E. / Voet, A.R.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - FlandersG0F9316N Belgium
Research Foundation - FlandersG051917N Belgium
Research Foundation - FlandersGBM-D3229-ASP/17 Belgium
CitationJournal: Protein Sci. / Year: 2020
Title: Influence of circular permutations on the structure and stability of a six-fold circular symmetric designer protein.
Authors: Mylemans, B. / Noguchi, H. / Deridder, E. / Lescrinier, E. / Tame, J.R.H. / Voet, A.R.D.
History
DepositionNov 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: v22Pizza6-AYW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3608
Polymers25,8001
Non-polymers5597
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-0 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.196, 56.892, 69.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein v22Pizza6-AYW


Mass: 25800.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 1.9 Å3/Da / Density % sol: 35.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Potassium bromide 28%(w/v) PEG2000 MME +15% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.45→44.14 Å / Num. obs: 34783 / % possible obs: 97.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.023 / Rrim(I) all: 0.084 / Net I/σ(I): 21.1
Reflection shellResolution: 1.45→1.47 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F0Q

6f0q


Resolution: 1.45→44.137 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.38
RfactorNum. reflection% reflection
Rfree0.2091 1712 4.93 %
Rwork0.1751 --
obs0.1768 34729 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→44.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 7 282 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012048
X-RAY DIFFRACTIONf_angle_d1.0762860
X-RAY DIFFRACTIONf_dihedral_angle_d3.452990
X-RAY DIFFRACTIONf_chiral_restr0.089363
X-RAY DIFFRACTIONf_plane_restr0.007383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.49270.30881310.28562659X-RAY DIFFRACTION96
1.4927-1.54090.29811320.26392681X-RAY DIFFRACTION97
1.5409-1.59590.29031360.23922653X-RAY DIFFRACTION96
1.5959-1.65980.28141420.22262693X-RAY DIFFRACTION97
1.6598-1.73540.22131500.20172705X-RAY DIFFRACTION97
1.7354-1.82690.23781380.19382728X-RAY DIFFRACTION98
1.8269-1.94130.21851430.18452733X-RAY DIFFRACTION98
1.9413-2.09120.2191430.17522769X-RAY DIFFRACTION98
2.0912-2.30170.21421520.17362756X-RAY DIFFRACTION99
2.3017-2.63470.20961400.17582800X-RAY DIFFRACTION99
2.6347-3.31930.19231620.15782843X-RAY DIFFRACTION99
3.3193-44.15780.16621430.14632997X-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