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- PDB-1m4j: CRYSTAL STRUCTURE OF THE N-TERMINAL ADF-H DOMAIN OF MOUSE TWINFIL... -

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Basic information

Entry
Database: PDB / ID: 1m4j
TitleCRYSTAL STRUCTURE OF THE N-TERMINAL ADF-H DOMAIN OF MOUSE TWINFILIN ISOFORM-1
ComponentsA6 gene product
KeywordsSTRUCTURAL PROTEIN / MIXED BETA-SHEET / PAIR OF ALPHA-HELICES
Function / homology
Function and homology information


regulation of actin phosphorylation / RHOBTB2 GTPase cycle / sequestering of actin monomers / negative regulation of actin filament polymerization / actin filament depolymerization / barbed-end actin filament capping / regulation of lamellipodium assembly / myofibril / positive regulation of cardiac muscle hypertrophy / actin monomer binding ...regulation of actin phosphorylation / RHOBTB2 GTPase cycle / sequestering of actin monomers / negative regulation of actin filament polymerization / actin filament depolymerization / barbed-end actin filament capping / regulation of lamellipodium assembly / myofibril / positive regulation of cardiac muscle hypertrophy / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / filopodium / actin filament / positive regulation of neuron projection development / cell-cell junction / actin filament binding / actin cytoskeleton / protein tyrosine kinase activity / protein-containing complex binding / perinuclear region of cytoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
Twinfilin / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPaavilainen, V.O. / Merckel, M.C. / Falck, S. / Ojala, P.J. / Pohl, E. / Wilmanns, M. / Lappalainen, P.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Structural Conservation Between the Actin Monomer-binding Sites of Twinfilin and Actin-depolymerizing Factor (ADF)/Cofilin
Authors: Paavilainen, V.O. / Merckel, M.C. / Falck, S. / Ojala, P.J. / Pohl, E. / Wilmanns, M. / Lappalainen, P.
#1: Journal: To be Published
Title: Twinfilin Forms a Stable Complex with ADP-Actin Monomers Through its Carboxyl-Terminal ADF-H Domain
Authors: Ojala, P.J. / Paavilainen, V.O. / Vartiainen, M.K. / Tuma, R. / Weeds, A.G. / Lappalainen, P.
#2: Journal: Mol.Cell.Biol. / Year: 2000
Title: Mouse A6/twinfilin is an actin monomer-binding protein that localizes to the regions of rapid actin dynamics
Authors: Vartiainen, M. / Ojala, P.J. / Auvinen, P. / Peranen, J. / Lappalainen, P.
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A6 gene product
B: A6 gene product


Theoretical massNumber of molelcules
Total (without water)32,5892
Polymers32,5892
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: A6 gene product


Theoretical massNumber of molelcules
Total (without water)16,2941
Polymers16,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.544, 74.488, 76.946
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 A6 gene product / TWINFILIN


Mass: 16294.358 Da / Num. of mol.: 2 / Fragment: N-terminal ADF-H Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: TWF / Plasmid: pGAT2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q91YR1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M Na-Citrate, 3% PEG 400, 0.1M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
250 mM1dropNaCl
310 mMTris1droppH7.5
41.6 Msodium citrate1reservoir
53 %PEG4001reservoir
60.1 Msodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8459 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 23, 2001 / Details: Premirrors, bent mirror
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8459 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 36771 / Num. obs: 36771 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044
Reflection shellResolution: 1.6→1.7 Å / Mean I/σ(I) obs: 4 / Num. unique all: 3101 / Rsym value: 0.255 / % possible all: 87.5
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. obs: 34257 / % possible obs: 93 % / Num. measured all: 457961
Reflection shell
*PLUS
Lowest resolution: 1.66 Å / % possible obs: 92.2 % / Rmerge(I) obs: 0.255

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: A MODEL BUILT INTO THE SAD MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 29973 -RANDOM
Rwork0.2315 ---
all0.2354 33286 --
obs0.2354 33286 90.5 %-
Displacement parametersBiso mean: 21.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 0 110 2276
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005016
X-RAY DIFFRACTIONc_angle_deg1.23684
X-RAY DIFFRACTIONc_dihedral_angle_d22.4946
X-RAY DIFFRACTIONc_improper_angle_d0.81569
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 280 9.4 %
Rwork0.231 4807 -
obs-3101 10 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 9 % / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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