[English] 日本語
Yorodumi
- PDB-6abr: Actin interacting protein 5 (Aip5, wild type) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6abr
TitleActin interacting protein 5 (Aip5, wild type)
ComponentsActin binding protein
KeywordsSTRUCTURAL PROTEIN
Function / homologycellular bud / cellular bud tip / positive regulation of actin filament bundle assembly / cellular bud neck / Glutaredoxin domain profile. / Thioredoxin-like superfamily / cytoplasm / Uncharacterized protein YFR016C
Function and homology information
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.002 Å
AuthorsSun, J. / Xie, Y. / Toh, J.D.W. / Hong, W. / MIao, Y. / Gao, Y.G.
CitationJournal: Nat Commun / Year: 2019
Title: Polarisome scaffolder Spa2-mediated macromolecular condensation of Aip5 for actin polymerization.
Authors: Xie, Y. / Sun, J. / Han, X. / Tursic-Wunder, A. / Toh, J.D.W. / Hong, W. / Gao, Y.G. / Miao, Y.
History
DepositionJul 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin binding protein
B: Actin binding protein


Theoretical massNumber of molelcules
Total (without water)28,5662
Polymers28,5662
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-6 kcal/mol
Surface area11080 Å2
Unit cell
Length a, b, c (Å)32.573, 82.775, 34.278
Angle α, β, γ (deg.)90.00, 107.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Actin binding protein


Mass: 14282.879 Da / Num. of mol.: 2 / Fragment: UNP residues 1110-1233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: YFR016C / Production host: Escherichia coli (E. coli) / References: UniProt: P43597
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.54 Å3/Da / Density % sol: 20.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCL pH 7.0, 20% PEG1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.000,0.9788,0.9636
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 29, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97881
30.96361
ReflectionResolution: 2→50 Å / Num. obs: 11332 / % possible obs: 96.8 % / Redundancy: 3.8 % / Rsym value: 0.052 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 943 / Rsym value: 0.142

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.002→32.715 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.93
RfactorNum. reflection% reflection
Rfree0.2618 1141 10.09 %
Rwork0.2264 --
obs0.23 11303 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→32.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 0 74 1552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071510
X-RAY DIFFRACTIONf_angle_d1.2932042
X-RAY DIFFRACTIONf_dihedral_angle_d15.639571
X-RAY DIFFRACTIONf_chiral_restr0.053221
X-RAY DIFFRACTIONf_plane_restr0.007264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0024-2.09350.30491340.23971194X-RAY DIFFRACTION93
2.0935-2.20390.27181410.22971250X-RAY DIFFRACTION95
2.2039-2.34190.29591390.22741283X-RAY DIFFRACTION97
2.3419-2.52270.28741450.24361256X-RAY DIFFRACTION97
2.5227-2.77640.27431450.2411293X-RAY DIFFRACTION98
2.7764-3.17790.2891470.23771299X-RAY DIFFRACTION98
3.1779-4.00270.23871440.22831291X-RAY DIFFRACTION98
4.0027-32.71970.23551460.20651296X-RAY DIFFRACTION97

+
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