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- PDB-1wy3: Chicken villin subdomain HP-35, K65(NLE), N68H, pH7.0 -

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Basic information

Entry
Database: PDB / ID: 1wy3
TitleChicken villin subdomain HP-35, K65(NLE), N68H, pH7.0
ComponentsVillin
KeywordsSTRUCTURAL PROTEIN / villin headgroup 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 / barbed-end actin filament capping / actin polymerization or depolymerization / 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 / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsChiu, T.K. / Kubelka, J. / Herbst-Irmer, R. / Eaton, W.A. / Hofrichter, J. / Davies, D.R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein.
Authors: Chiu, T.K. / Kubelka, J. / Herbst-Irmer, R. / Eaton, W.A. / Hofrichter, J. / Davies, D.R.
History
DepositionFeb 4, 2005Deposition site: PDBJ / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 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


Theoretical massNumber of molelcules
Total (without water)4,0731
Polymers4,0731
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)19.689, 40.022, 75.148
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-1037-

HOH

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Components

#1: Protein/peptide Villin


Mass: 4072.729 Da / Num. of mol.: 1 / Fragment: VHP / Mutation: K65(NLE), N68H / Source method: obtained synthetically
Details: synthetic peptide, sequence corresponds to Chicken Villin residues 792-826, residue 65 is norleucine (lysine without terminal NH3 group)
References: UniProt: P02640
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.8 Å3/Da / Density % sol: 31.8 %
Crystal growTemperature: 293 K / pH: 7
Details: 1ul 50mg/ml peptide plus 1ul (200mM KFormate, 20% PEG3350), pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.00

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.95→30 Å / Num. obs: 17326 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 16.3 % / Rsym value: 0.064 / Net I/σ(I): 20.5
Reflection shellResolution: 0.95→0.98 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.213 / % possible all: 57.6

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Processing

Software
NameClassification
MAR345data collection
HKL-2000data reduction
EPMRphasing
SHELXL-97refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YRF

1yrf


Resolution: 0.95→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC B-VALUE FOR ALL ATOMS RIDING HYDROGENS; RESIDUE 65 IS NORLEUCINE (LYSINE WITHOUT TERMINAL NH3 GROUP) SHELX: DEFS 0.02 0.02 0.01, SIMU 0.05, ISOR 0.05, WGHT 0.25, SWAT.
RfactorNum. reflectionSelection details
Rfree0.171 666 RANDOM
obs0.145 --
all-17315 -
Displacement parametersBiso mean: 14.8 Å2
Refinement stepCycle: LAST / Resolution: 0.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms605 0 0 51 656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0.02
X-RAY DIFFRACTIONs_from_restr_planes0.02
X-RAY DIFFRACTIONs_zero_chiral_vol0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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