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- PDB-2f4k: Chicken villin subdomain HP-35, K65(NLE), N68H, K70(NLE), PH9 -

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Basic information

Entry
Database: PDB / ID: 2f4k
TitleChicken villin subdomain HP-35, K65(NLE), N68H, K70(NLE), PH9
ComponentsVillin-1
KeywordsSTRUCTURAL PROTEIN / Villin head group subdomain
Function / homology
Function and homology information


regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / actin filament depolymerization ...regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / cellular response to hepatocyte growth factor stimulus / positive regulation of epithelial cell migration / actin filament bundle / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / microvillus / cellular response to epidermal growth factor stimulus / ruffle / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / filopodium / response to bacterium / epidermal growth factor receptor signaling pathway / actin filament binding / actin cytoskeleton / lamellipodium / regulation of cell shape / positive regulation of cell migration / calcium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Gelsolin-like domain superfamily / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.05 Å
AuthorsChiu, T.K. / Davies, D.R. / Kubelka, J. / Hofrichter, J. / Eaton, W.A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Sub-microsecond Protein Folding.
Authors: Kubelka, J. / Chiu, T.K. / Davies, D.R. / Eaton, W.A. / Hofrichter, J.
History
DepositionNov 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Villin-1


Theoretical massNumber of molelcules
Total (without water)4,0571
Polymers4,0571
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)19.677, 39.901, 75.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-120-

HOH

21A-124-

HOH

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Components

#1: Protein/peptide Villin-1


Mass: 4056.707 Da / Num. of mol.: 1 / Fragment: residues 792-826 / Mutation: N68H / Source method: obtained synthetically
Details: This sequence occurs naturally in Gallus gallus (chicken).
References: UniProt: P02640
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.82 Å3/Da / Density % sol: 32.27 %
Crystal growDetails: Initial drop contained 1ul 90mg/ml protein in 10mM Tris (pH7.4) and 7.5% v/v trifluoroethanol (TFE) and 1ul reservoir solution. Precipitant in reservoir was (initial: 800mM AmSO4, 100mM ...Details: Initial drop contained 1ul 90mg/ml protein in 10mM Tris (pH7.4) and 7.5% v/v trifluoroethanol (TFE) and 1ul reservoir solution. Precipitant in reservoir was (initial: 800mM AmSO4, 100mM Bicine (pH 9.0), 10% v/v TFE) and (final: 1.6M AmSO4, 100mM Bicine (pH 9.0), 7.5% v/v TFE). Reservoir solution was changed from initial to final after one week.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 22-ID11
ROTATING ANODE21.54
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJul 26, 2005
MARRESEARCH2AREA DETECTORJul 16, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.541
ReflectionResolution: 1.05→20 Å / Num. obs: 13770 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 22.5
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3 / % possible all: 74.3

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: 1WY3 WITHOUT SOLVENT

1wy3


Resolution: 1.05→20 Å / Num. parameters: 3238 / Num. restraintsaints: 4064 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: STARTING MODEL WAS REFINED BY RIGID- BODY AND TORSION-ANGLE REFINEMENT IN CNS. TWO DATASETS WERE COLLECTED, ONE AT NIH AND OTHER BY MAIL-IN-CR AT APS BEAMLINE 22-ID AND FINALLY MERGED. ...Details: STARTING MODEL WAS REFINED BY RIGID- BODY AND TORSION-ANGLE REFINEMENT IN CNS. TWO DATASETS WERE COLLECTED, ONE AT NIH AND OTHER BY MAIL-IN-CR AT APS BEAMLINE 22-ID AND FINALLY MERGED. ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 WHICH REDUCED FREE R USING SHELX. SHELXL parameters: DEFS 0.02 0.02 0.01 0.04, SIMU 0.05, ISOR 0.2, HOPE, SWAT, ANIS, WGHT 0.25
RfactorNum. reflection% reflectionSelection details
Rfree0.166 698 5.4 %RANDOM
all0.14 13042 --
obs0.14 -90.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 275 / Occupancy sum non hydrogen: 336.5
Refinement stepCycle: LAST / Resolution: 1.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 0 53 654
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.018
X-RAY DIFFRACTIONs_zero_chiral_vol0.008
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.007
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.043
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.114

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