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- PDB-1yrf: Chicken villin subdomain HP-35, N68H, pH6.7 -

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Basic information

Entry
Database: PDB / ID: 1yrf
TitleChicken villin subdomain HP-35, N68H, pH6.7
ComponentsVillin
KeywordsSTRUCTURAL PROTEIN / villin headpiece 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
ACETATE ION / Villin-1
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.07 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 3, 2005Deposition site: RCSB / 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 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Villin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2443
Polymers4,0891
Non-polymers1552
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.155, 32.155, 56.863
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-64-

TRP

21A-64-

TRP

31A-1049-

HOH

41A-1060-

HOH

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Components

#1: Protein/peptide Villin


Mass: 4088.751 Da / Num. of mol.: 1 / Fragment: VHP / Mutation: N68H / Source method: obtained synthetically
Details: Sequence corresponds to Chicken Villin residues 792-826
References: UniProt: P02640
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.07 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 293 K / pH: 6.7
Details: 1ul 100mg/ml peptide plus 1ul (200mM NaOAc, 2.2M AmSO4), pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.70

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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: 1.07→30 Å / Num. obs: 15545 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 19.8 % / Rsym value: 0.043 / Net I/σ(I): 50.3
Reflection shellResolution: 1.07→1.11 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.423 / % possible all: 99.9

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Processing

Software
NameClassification
MAR345data collection
HKL-2000data reduction
SOLVEphasing
SHELXL-97refinement
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.07→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: INDIVIDUAL ANISOTROPIC B FOR ALL NONHYDROGENS, HYDROGEN ADDED AS 'RIDING HYDROGENS' SHELX: DEFS 0.02 0.1 0.02, SIMU 0.1, ISOR 0.03, WGHT 0.2, SWAT. THE SIDE-CHAIN OF TRP64 IS IN 2 ...Details: INDIVIDUAL ANISOTROPIC B FOR ALL NONHYDROGENS, HYDROGEN ADDED AS 'RIDING HYDROGENS' SHELX: DEFS 0.02 0.1 0.02, SIMU 0.1, ISOR 0.03, WGHT 0.2, SWAT. THE SIDE-CHAIN OF TRP64 IS IN 2 CONFORMATIONS, THE FIRST CONFORMATION PARTIALLY OVERLAP EACH OTHER ON A 2-FOLD AXIS.
RfactorNum. reflectionSelection details
Rfree0.161 622 RANDOM
obs0.155 --
all-15534 -
Displacement parametersBiso mean: 18.2 Å2
Refinement stepCycle: LAST / Resolution: 1.07→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms639 0 31 61 731
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_planes0.1
X-RAY DIFFRACTIONs_zero_chiral_vol0.1

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