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- PDB-1cof: YEAST COFILIN, ORTHORHOMBIC CRYSTAL FORM -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1cof
TitleYEAST COFILIN, ORTHORHOMBIC CRYSTAL FORM
ComponentsCOFILINADF/Cofilin family
KeywordsACTIN-BINDING PROTEIN / ACTIN-BINDING / CYTOSKELETON
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 / MIR / Resolution: 2.3 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: Mol.Cell.Biol. / Year: 1995
Title: The Adf/Cofilin Proteins: Stimulus-Responsive Modulators of Actin Dynamics
Authors: Moon, A. / Drubin, D.G.
History
DepositionNov 26, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: COFILIN


Theoretical massNumber of molelcules
Total (without water)15,9201
Polymers15,9201
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.669, 48.773, 101.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.97 Å3/Da / Density % sol: 38 %
Crystal growpH: 7.2 / Details: CRYSTALLIZED FROM 25% PEG 4000 SOLUTION., pH 7.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 7
Components of the solutions
*PLUS
Conc.: 20-30 % / Common name: PEG4000

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→26.2 Å / Num. obs: 6330 / % possible obs: 87.5 % / Observed criterion σ(I): 2 / Redundancy: 2.33 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.5
Reflection
*PLUS
Rmerge(I) obs: 0.067

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Processing

Software
NameClassification
PHASESphasing
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→8 Å / σ(F): 2
Details: N-TERMINAL RESIDUES 1 - 5 AND C-TERMINAL RESIDUES 141 - 143 ARE NOT VISIBLE IN THE MAPS. LOOP 73 - 78 HAS WEAK ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rwork0.184 --
obs-5696 81.1 %
Displacement parametersBiso mean: 25.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 0 32 1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.018
X-RAY DIFFRACTIONp_angle_d0.0270.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.1041.5
X-RAY DIFFRACTIONp_mcangle_it4.8462
X-RAY DIFFRACTIONp_scbond_it4.9252
X-RAY DIFFRACTIONp_scangle_it7.4593
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1270.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.180.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1710.3
X-RAY DIFFRACTIONp_planar_tor1.42
X-RAY DIFFRACTIONp_staggered_tor17.910
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor15.710
X-RAY DIFFRACTIONp_special_tor
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: PROFFT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.61
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg24.53
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.45

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