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- PDB-4kef: Structure of Cofilin Mutant (cof1-159p) -

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Basic information

Entry
Database: PDB / ID: 4kef
TitleStructure of Cofilin Mutant (cof1-159p)
ComponentsCofilinADF/Cofilin family
KeywordsActin Binding Protein / Actin Depolymerization Factor
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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

#1: Protein Cofilin / ADF/Cofilin family / 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 / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 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

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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

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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

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