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- PDB-4ked: Crystal Structure of Cofilin Mutant (cof1-157p) -

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Basic information

Entry
Database: PDB / ID: 4ked
TitleCrystal Structure of Cofilin Mutant (cof1-157p)
ComponentsCofilin
KeywordsActin Binding Protein / Actin Depolymerization Factor
Function / homology
Function and homology information


actin cortical patch / actin filament severing / Golgi to plasma membrane protein transport / 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: 1.901 Å
AuthorsKish-Trier, E. / Haarer, B. / Cingolani, G. / Amberg, D.C.
CitationJournal: To be Published
Title: Crystal Structure of Cofilin Mutant (cof1-157p)
Authors: Kish-Trier, E. / Haarer, B. / Cingolani, G. / Amberg, D.C.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 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
B: Cofilin


Theoretical massNumber of molelcules
Total (without water)31,6072
Polymers31,6072
Non-polymers00
Water3,729207
1
A: Cofilin


Theoretical massNumber of molelcules
Total (without water)15,8031
Polymers15,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cofilin


Theoretical massNumber of molelcules
Total (without water)15,8031
Polymers15,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.023, 30.325, 104.268
Angle α, β, γ (deg.)90.00, 133.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cofilin / Actin-depolymerizing factor 1


Mass: 15803.492 Da / Num. of mol.: 2 / Mutation: R135D
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.: 207 / 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: 2.74 Å3/Da / Density % sol: 55.17 %
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: X25 / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 50075 / % possible obs: 94.68 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 3.8 % / Biso Wilson estimate: 31.84 Å2 / Rsym value: 0.049

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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: 1.901→27.427 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1959 7.36 %
Rwork0.1807 --
obs0.1845 26623 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→27.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 0 207 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072110
X-RAY DIFFRACTIONf_angle_d0.9722852
X-RAY DIFFRACTIONf_dihedral_angle_d11.738768
X-RAY DIFFRACTIONf_chiral_restr0.073322
X-RAY DIFFRACTIONf_plane_restr0.004364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9013-1.94880.31341240.26161422X-RAY DIFFRACTION80
1.9488-2.00150.28431220.20761686X-RAY DIFFRACTION93
2.0015-2.06030.21371370.19041739X-RAY DIFFRACTION97
2.0603-2.12680.24071590.17911764X-RAY DIFFRACTION97
2.1268-2.20280.23591190.17991776X-RAY DIFFRACTION98
2.2028-2.2910.25431500.19121721X-RAY DIFFRACTION95
2.291-2.39520.24611440.18831781X-RAY DIFFRACTION99
2.3952-2.52140.23191440.18841821X-RAY DIFFRACTION99
2.5214-2.67920.23471370.19211811X-RAY DIFFRACTION99
2.6792-2.88590.2161490.18661811X-RAY DIFFRACTION100
2.8859-3.17590.2021350.18821840X-RAY DIFFRACTION100
3.1759-3.63450.22541500.17651842X-RAY DIFFRACTION100
3.6345-4.57570.21731490.15271848X-RAY DIFFRACTION99
4.5757-27.43010.25621400.18471802X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4046-0.45340.35660.8510.16860.7692-0.00310.09430.10220.0566-0.0314-0.0722-0.22760.3102-0.00020.2628-0.0283-0.03260.20890.01510.1618-67.134925.7995105.5918
21.0489-0.74990.06840.7080.28420.54570.09890.2416-0.1025-0.4157-0.01460.23230.27980.10730.02890.31190.0096-0.05140.230.00370.1549-72.209718.687199.2451
30.0367-0.03140.05360.4408-0.08090.0874-0.02770.433-0.008-0.4547-0.2173-0.42130.06620.3407-0.61880.15450.24940.2460.78310.1390.2092-58.160422.901193.8069
40.62090.29610.23650.3075-0.30271.16230.30990.251-0.4501-0.7284-0.10690.0820.63590.3076-0.00980.51390.0403-0.10680.2687-0.03630.3277-73.010813.832996.7046
50.8114-0.1743-0.08840.695-0.28950.1736-0.0816-0.23720.57340.11240.04750.0459-0.15810.07050.00270.1949-0.0160.02380.2581-0.05480.3408-100.30524.398279.7987
60.4698-0.1652-0.28280.4387-0.45690.846-0.1338-0.0082-0.1475-0.00360.0878-0.23680.19770.4168-0.00360.1613-0.02310.0280.30670.01380.3057-93.230217.040575.9362
70.13350.01750.03940.24030.09090.0463-0.0182-0.488-0.29320.7920.2365-0.62380.08840.1154-0.01360.5186-0.0356-0.11440.7136-0.01680.4216-90.241821.266890.7597
80.2107-0.01230.01920.23780.15540.2638-0.3506-0.2151-0.80150.08530.0417-0.34960.56540.1723-0.00590.29850.01680.07920.33940.0530.5297-90.581412.525175.5505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 111 )
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 137 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 56 )
6X-RAY DIFFRACTION6chain 'B' and (resid 57 through 94 )
7X-RAY DIFFRACTION7chain 'B' and (resid 95 through 111 )
8X-RAY DIFFRACTION8chain 'B' and (resid 112 through 137 )

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