[English] 日本語
Yorodumi
- PDB-6yjj: Structure of CYRI-B (FAM49B) from Rhincodon typus (selenomethioni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yjj
TitleStructure of CYRI-B (FAM49B) from Rhincodon typus (selenomethionine derivative)
ComponentsCYRI-B (FAM49B)
KeywordsCYTOSOLIC PROTEIN / CYRI-B / FAM49B / actin assembly / Rac binding protein / cell motility regulator
Biological speciesRhincodon typus (whale shark)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKaplan, E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N000994/1 United Kingdom
Wellcome Trust101828/Z/13/Z United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structure of CYRI-B (FAM49B), a key regulator of cellular actin assembly.
Authors: Kaplan, E. / Stone, R. / Hume, P.J. / Greene, N.P. / Koronakis, V.
History
DepositionApr 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: 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_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYRI-B (FAM49B)


Theoretical massNumber of molelcules
Total (without water)37,3791
Polymers37,3791
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.400, 72.820, 107.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CYRI-B (FAM49B)


Mass: 37378.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhincodon typus (whale shark) / Gene: fam49b / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.31 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.1 M Bis-Tris pH 5.5 and 0.2 M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9611 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2.4→72.82 Å / Num. obs: 13006 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.042 / Rrim(I) all: 0.13 / Net I/σ(I): 12.8 / Num. measured all: 123774 / Scaling rejects: 39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.498.21.0321088913290.7820.3821.1022.1100
8.98-72.828.10.05224853080.9970.0180.05536.799.9

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.25data extraction
PHENIX1.14_3260refinement
REFMAC7.0.078refinement
PHASERphasing
Aimless0.7.3data scaling
iMOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→53.66 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 638 4.92 %RANDOM
Rwork0.2048 12321 --
obs0.2067 12959 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.31 Å2 / Biso mean: 63.28 Å2 / Biso min: 23.68 Å2
Refinement stepCycle: final / Resolution: 2.4→53.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 0 8 2564
Biso mean---42.51 -
Num. residues----320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4-2.58530.32821200.28142405
2.5853-2.84550.33411260.25432410
2.8455-3.25720.2831390.23272425
3.2572-4.10350.23561260.19782483
4.1035-53.660.19551270.17582598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.32710.13651.64342.14281.46225.8316-0.0797-0.31920.29580.3059-0.0893-0.0207-0.0831-0.5490.14960.3650.00090.00490.2776-0.0280.41073.698813.9862-26.043
22.1457-0.23081.57982.4619-0.82475.28160.0597-0.0313-0.0055-0.1137-0.1071-0.01260.82540.20310.02780.4656-0.00140.02630.2858-0.02940.442613.39084.2093-20.8678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 164 )A0 - 164
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 324 )A165 - 324

+
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