[English] 日本語
Yorodumi
- PDB-4kef: Structure of Cofilin Mutant (cof1-159p) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kef
TitleStructure of Cofilin Mutant (cof1-159p)
ComponentsCofilin
KeywordsActin Binding Protein / Actin Depolymerization Factor
Function / homology
Function and homology information


actin cortical patch / actin filament severing / actin filament depolymerization / Golgi to plasma membrane protein transport / actin filament organization / nuclear matrix / endocytosis / actin filament binding / actin cytoskeleton / plasma membrane / cytoplasm
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.098 Å
AuthorsKish-Trier, E. / Haarer, B. / Cingolani, G. / Amberg, D.C.
CitationJournal: To be Published
Title: Structure of Cofilin Mutant (cof1-159p)
Authors: Kish-Trier, E. / Haarer, B. / Cingolani, G. / Amberg, D.C.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cofilin


Theoretical massNumber of molelcules
Total (without water)15,8321
Polymers15,8321
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.096, 69.544, 32.048
Angle α, β, γ (deg.)90.00, 100.56, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cofilin / Actin-depolymerizing factor 1


Mass: 15831.506 Da / Num. of mol.: 1 / Mutation: K82D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: COF1, YLL050C, L0596 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03048
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% PEG4000, 150mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.098→30 Å / Num. obs: 49213 / % possible obs: 99.77 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 2.8 / Redundancy: 4.2 % / Biso Wilson estimate: 10.45 Å2 / Rsym value: 0.076 / Net I/σ(I): 2.8
Reflection shellResolution: 1.098→1.14 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 205008 / Rsym value: 0.345 / % possible all: 98.99

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.098→28.697 Å / WRfactor Rfree: 0.1443 / WRfactor Rwork: 0.1265 / SU ML: 0.09 / σ(F): 0 / Phase error: 13.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1443 1907 4.04 %Random
Rwork0.1265 ---
obs0.1272 47198 95.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.098→28.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1049 0 0 184 1233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111127
X-RAY DIFFRACTIONf_angle_d1.4081541
X-RAY DIFFRACTIONf_dihedral_angle_d11.926432
X-RAY DIFFRACTIONf_chiral_restr0.083176
X-RAY DIFFRACTIONf_plane_restr0.007198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0977-1.12520.20441260.18662922X-RAY DIFFRACTION86
1.1252-1.15560.19041240.15992984X-RAY DIFFRACTION89
1.1556-1.18960.18351350.13623112X-RAY DIFFRACTION92
1.1896-1.2280.14811270.12613144X-RAY DIFFRACTION93
1.228-1.27190.15211330.11843192X-RAY DIFFRACTION94
1.2719-1.32280.13241340.113201X-RAY DIFFRACTION95
1.3228-1.3830.15731310.10553249X-RAY DIFFRACTION96
1.383-1.45590.14951390.10373280X-RAY DIFFRACTION98
1.4559-1.54710.12861420.09633330X-RAY DIFFRACTION98
1.5471-1.66660.12551420.10533335X-RAY DIFFRACTION99
1.6666-1.83430.13241420.10523337X-RAY DIFFRACTION99
1.8343-2.09960.12991430.11273380X-RAY DIFFRACTION100
2.0996-2.6450.14481430.12543389X-RAY DIFFRACTION100
2.645-28.70730.14721460.14893436X-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