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- PDB-4kee: Crystal Structure of Cofilin Mutant (cof1-158p) -

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Basic information

Entry
Database: PDB / ID: 4kee
TitleCrystal Structure of Cofilin Mutant (cof1-158p)
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: 1.448 Å
AuthorsKish-Trier, E. / Haarer, B. / Cingolani, G. / Amberg, D.C.
CitationJournal: To be Published
Title: Crystal Structure of Cofilin Mutant (cof1-158p)
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)15,8181
Polymers15,8181
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.119, 69.852, 32.164
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cofilin / Actin-depolymerizing factor 1


Mass: 15817.518 Da / Num. of mol.: 1 / Mutation: R80E
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.: 172 / 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: 1.96 Å3/Da / Density % sol: 37.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% PEG 4000, 150mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.448→50 Å / Num. obs: 20869 / % possible obs: 95.98 % / Observed criterion σ(F): 3.2 / Observed criterion σ(I): 3.2 / Redundancy: 6.5 % / Biso Wilson estimate: 10.61 Å2 / Rsym value: 0.11 / Net I/σ(I): 2.7
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.537 / % possible all: 72.34

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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: 1.448→14.942 Å / WRfactor Rfree: 0.1748 / WRfactor Rwork: 0.1354 / SU ML: 0.11 / σ(F): 0 / Phase error: 16.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1748 1928 9.56 %Random
Rwork0.1354 ---
obs0.1391 20166 92.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.448→14.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 0 172 1211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031058
X-RAY DIFFRACTIONf_angle_d0.8351429
X-RAY DIFFRACTIONf_dihedral_angle_d11.382385
X-RAY DIFFRACTIONf_chiral_restr0.051160
X-RAY DIFFRACTIONf_plane_restr0.003183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.448-1.48420.2584920.1692888X-RAY DIFFRACTION63
1.4842-1.52430.18811120.13651004X-RAY DIFFRACTION73
1.5243-1.56910.21531260.13821188X-RAY DIFFRACTION85
1.5691-1.61970.18251370.12921299X-RAY DIFFRACTION93
1.6197-1.67750.18341460.11831333X-RAY DIFFRACTION96
1.6775-1.74460.1581390.11981359X-RAY DIFFRACTION96
1.7446-1.82390.16351380.12171350X-RAY DIFFRACTION97
1.8239-1.91980.18821430.12231390X-RAY DIFFRACTION98
1.9198-2.03980.16631500.11861408X-RAY DIFFRACTION99
2.0398-2.19690.15691460.12111380X-RAY DIFFRACTION100
2.1969-2.41710.16271490.12571406X-RAY DIFFRACTION100
2.4171-2.7650.17531480.14351395X-RAY DIFFRACTION99
2.765-3.47630.17191510.14591412X-RAY DIFFRACTION100
3.4763-14.94250.17831510.15051426X-RAY DIFFRACTION100

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