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- PDB-2w0i: Structure Of C-Terminal Actin Depolymerizing Factor Homology (Adf... -

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Basic information

Entry
Database: PDB / ID: 2w0i
TitleStructure Of C-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain Of Human Twinfilin-2
ComponentsTWINFILIN-2
KeywordsTRANSFERASE / CYTOSKELETON / ACTIN-BINDING / ACTIN BINDING / COFILIN-LIKE / PHOSPHOPROTEIN / PHOSPHORYLATION / PROTEIN TYROSINE KINASE-9 / ACTIN DEPOLYMERIZING FACTOR
Function / homology
Function and homology information


regulation of microvillus length / sequestering of actin monomers / negative regulation of actin filament polymerization / stereocilium / cell projection organization / actin filament depolymerization / barbed-end actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / regulation of lamellipodium assembly / Sensory processing of sound by inner hair cells of the cochlea ...regulation of microvillus length / sequestering of actin monomers / negative regulation of actin filament polymerization / stereocilium / cell projection organization / actin filament depolymerization / barbed-end actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / regulation of lamellipodium assembly / Sensory processing of sound by inner hair cells of the cochlea / myofibril / actin monomer binding / positive regulation of axon extension / positive regulation of lamellipodium assembly / cellular response to retinoic acid / phosphatidylinositol-4,5-bisphosphate binding / filopodium / actin filament / regulation of actin cytoskeleton organization / protein kinase C binding / cellular response to growth factor stimulus / positive regulation of neuron projection development / actin filament binding / lamellipodium / growth cone / cadherin binding / perinuclear region of cytoplasm / RNA binding / extracellular exosome / ATP binding / cytoplasm
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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsElkins, J.M. / Pike, A.C.W. / Salah, E. / Savitsky, P. / Murray, J.W. / Roos, A. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Wikstrom, M. ...Elkins, J.M. / Pike, A.C.W. / Salah, E. / Savitsky, P. / Murray, J.W. / Roos, A. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Wikstrom, M. / Bountra, C. / Knapp, S.
CitationJournal: To be Published
Title: Structure of C-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin- 2
Authors: Elkins, J.M. / Pike, A.C.W. / Salah, E. / Savitsky, P. / Murray, J.W. / Roos, A. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Wikstrom, M. / Bountra, C. / Knapp, S.
History
DepositionAug 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 20, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TWINFILIN-2


Theoretical massNumber of molelcules
Total (without water)15,7181
Polymers15,7181
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.308, 64.308, 136.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein TWINFILIN-2 / TWINFILIN-1-LIKE PROTEIN / A6-RELATED PROTEIN / PROTEIN TYROSINE KINASE 9-LIKE


Mass: 15717.939 Da / Num. of mol.: 1
Fragment: ACTIN DEPOLYMERIZING FACTOR HOMOLOGY (ADF-H) DOMAIN 2, RESIDUES 181-313
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: Y309D IS A CLONING ARTEFACT / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q6IBS0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsY309D IS A CLONING ARTEFACT

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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.5 / Details: 2.6M SODIUM MALONATE, 0.1M BISTRIS PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99186
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99186 Å / Relative weight: 1
ReflectionResolution: 1.8→55.64 Å / Num. obs: 16080 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 21.81 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1VKK, 2VAS, 1M4J.

1vkk

2vas

1m4j


Resolution: 1.8→43.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.236 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1067 6.6 %RANDOM
Rwork0.186 ---
obs0.189 15008 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 0 71 1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221112
X-RAY DIFFRACTIONr_bond_other_d0.0070.02764
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9781505
X-RAY DIFFRACTIONr_angle_other_deg0.97831872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7245134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77423.92251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20915204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.565157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined0.1990.2217
X-RAY DIFFRACTIONr_nbd_other0.2260.2686
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2531
X-RAY DIFFRACTIONr_nbtor_other0.1110.2504
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8673680
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.27151105
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.8728432
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.50611400
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 93
Rwork0.256 1040
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)
11.81420.7869-0.04166.3364-0.44930.94690.1752-0.0488-0.12230.6463-0.0205-0.073-0.0938-0.109-0.15480.0943-0.0331-0.0650.06470.01160.003215.278-21.271-2.112
26.0837-1.8073.734410.0109-1.63555.5810.3771-0.1852-0.58990.6503-0.08930.49170.3556-0.0256-0.28780.069-0.0356-0.056-0.00140.02210.035912.142-31.197-1.154
310.2997-0.18664.99093.3973-0.51625.78290.429-0.1622-0.86540.18580.06820.06690.47390.0158-0.49720.1619-0.0129-0.13230.0040.01150.131811.453-32.621-5.352
410.1856-0.28888.9021.5884-1.26269.85610.80830.68170.2109-0.6254-0.5332-0.10181.3010.4447-0.27510.4070.12180.00230.03930.0141-0.153511.991-25.268-18.514
55.1707-0.11280.13137.7807-1.26053.50140.3818-0.1486-0.5202-0.0241-0.1125-0.65030.40340.2229-0.26930.05020.0406-0.1233-0.05-0.02310.095116.788-34.368-4.563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 230
2X-RAY DIFFRACTION2A231 - 245
3X-RAY DIFFRACTION3A246 - 264
4X-RAY DIFFRACTION4A265 - 278
5X-RAY DIFFRACTION5A279 - 313

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