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- PDB-2i2q: Fission Yeast cofilin -

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Basic information

Entry
Database: PDB / ID: 2i2q
TitleFission Yeast cofilin
ComponentsCofilinADF/Cofilin family
Keywordsactin-binding protein / N-terminal Serine
Function / homology
Function and homology information


negative regulation of actin filament binding / actin filament debranching / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / actin nucleation / cell tip / actin cortical patch / actin filament severing / actin filament depolymerization ...negative regulation of actin filament binding / actin filament debranching / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / actin nucleation / cell tip / actin cortical patch / actin filament severing / actin filament depolymerization / cell division site / actin monomer binding / nuclear matrix / actin filament binding / actin cytoskeleton / 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 speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsAndrianantoandro, E. / Pollard, T.D.
CitationJournal: Mol.Cell / Year: 2006
Title: Mechanism of Actin Filament Turnover by Severing and Nucleation at Different Concentrations of ADF/Cofilin.
Authors: Andrianantoandro, E. / Pollard, T.D.
History
DepositionAug 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cofilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3118
Polymers15,6411
Non-polymers6707
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.915, 81.915, 61.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cofilin / ADF/Cofilin family


Mass: 15640.864 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cof1 / Production host: Escherichia coli (E. coli) / References: UniProt: P78929
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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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: 3.32 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.1 M Ammonium Sulfate, 100 mM imidazole pH 7.0, 1 mM NiSO4, 2.5% PEG 400, 1 mM LDAO, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 25210 / % possible obs: 88.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.071 / Χ2: 5.212 / Net I/σ(I): 18.5
Reflection shellResolution: 1.6→1.66 Å / Num. unique all: 981 / Χ2: 7.956 / % possible all: 35.4

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.499 / Packing: 0.381
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral91.7 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COF

1cof


Resolution: 1.72→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2059 9 %Random
Rwork0.236 ---
all0.246 22932 --
obs0.241 20784 90.6 %-
Solvent computationBsol: 52.597 Å2
Displacement parametersBiso mean: 30.406 Å2
Baniso -1Baniso -2Baniso -3
1-1.398 Å20 Å20 Å2
2--1.398 Å20 Å2
3----2.797 Å2
Refinement stepCycle: LAST / Resolution: 1.72→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 42 90 1106
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3721.5
X-RAY DIFFRACTIONc_scbond_it2.1362
X-RAY DIFFRACTIONc_mcangle_it2.1742
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shell
Resolution (Å)Refine-ID% reflection obs (%)
1.6-1.66X-RAY DIFFRACTION35.4
1.66-1.72X-RAY DIFFRACTION72
1.72-1.8X-RAY DIFFRACTION92.6
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2so4.param
X-RAY DIFFRACTION3lda.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5egl.param

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