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- PDB-1qpv: YEAST COFILIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1qpv
TitleYEAST COFILIN
ComponentsYEAST COFILINADF/Cofilin family
KeywordsACTIN-BINDING PROTEIN / THREE LAYERS:ALPHA/MIXED BETA/ALPHA / COFILIN FOLD
Function / homology
Function and homology information


actin cortical patch / Golgi to plasma membrane protein transport / actin filament severing / actin filament depolymerization / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFedorov, A.A. / Lappalainen, P. / Fedorov, E.V. / Drubin, D.G. / Almo, S.C.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure determination of yeast cofilin.
Authors: Fedorov, A.A. / Lappalainen, P. / Fedorov, E.V. / Drubin, D.G. / Almo, S.C.
#1: Journal: Embo J. / Year: 1997
Title: Essential Functions and Actin-Binding Surfaces of Yeast Cofilin Revealed by Systematic Mutagenesis
Authors: Lappalainen, P. / Fedorov, E.V. / Fedorov, A.A. / Almo, S.C. / Drubin, D.G.
#2: Journal: Nature / Year: 1997
Title: Cofilin Promotes Rapid Actin Filament Turnover in Vivo
Authors: Lappalainen, P. / Drubin, D.G.
History
DepositionMay 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YEAST COFILIN


Theoretical massNumber of molelcules
Total (without water)15,9201
Polymers15,9201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.780, 46.043, 87.703
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is monomer

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Components

#1: Protein YEAST COFILIN / ADF/Cofilin family


Mass: 15919.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: Q03048

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 4000 , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 15, 1995
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→25.2 Å / Num. all: 2529 / Num. obs: 2377 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4.9 / % possible all: 77.4

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1COF

1cof


Resolution: 3→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 210 10 %RANDOM
Rwork0.202 ---
all0.228 2303 --
obs0.209 2138 82.9 %-
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 0 0 1057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.003
X-RAY DIFFRACTIONx_angle_deg0.63
X-RAY DIFFRACTIONx_dihedral_angle_d28.71
X-RAY DIFFRACTIONx_improper_angle_d0.398
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO

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