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- PDB-1f7s: CRYSTAL STRUCTURE OF ADF1 FROM ARABIDOPSIS THALIANA -

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Basic information

Entry
Database: PDB / ID: 1f7s
TitleCRYSTAL STRUCTURE OF ADF1 FROM ARABIDOPSIS THALIANA
ComponentsACTIN DEPOLYMERIZING FACTOR (ADF)
KeywordsPLANT PROTEIN / KINK IN ALPHA-HELIX 3
Function / homology
Function and homology information


actin filament depolymerization / actin cytoskeleton / actin binding / 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
Actin-depolymerizing factor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBowman, G.D. / Nodelman, I.M. / Lindberg, U. / Chua, N.H. / Schutt, C.E.
CitationJournal: Proteins / Year: 2000
Title: A comparative structural analysis of the ADF/cofilin family.
Authors: Bowman, G.D. / Nodelman, I.M. / Hong, Y. / Chua, N.H. / Lindberg, U. / Schutt, C.E.
History
DepositionJun 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: ACTIN DEPOLYMERIZING FACTOR (ADF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3662
Polymers16,1371
Non-polymers2291
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.873, 71.308, 63.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ACTIN DEPOLYMERIZING FACTOR (ADF)


Mass: 16136.562 Da / Num. of mol.: 1 / Fragment: ACTIN BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / Keywords: DISORDERED C-TERMINAL HELIX / References: UniProt: Q39250
#2: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 37.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Ammonium sulfate, sodium citrate, LDAO, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mMpotassium phosphate1drop
20.4 mMdithiothreitol1drop
37.2-10 mg/mlprotein1drop
40.8 Mammonium sulfate1drop
550 mMcitrate1drop
62 mMLDAO1drop
71.6 Mammonium sulfate1reservoir
8100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25.8 Å / Num. all: 60228 / Num. obs: 8926 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.135 / % possible all: 98.4
Reflection
*PLUS
Num. measured all: 60228
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2→26 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 887 RANDOM
Rwork0.21 --
all0.214 8836 -
obs0.214 8836 -
Refinement stepCycle: LAST / Resolution: 2→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 16 89 1086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_torsion_impr_deg0.62
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 26 Å / σ(F): 1 / % reflection Rfree: 10 % / Rfactor obs: 0.211 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2

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