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- PDB-5i1p: Villin headpiece subdomain with a Lys30 to beta-3-homolysine subs... -

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Basic information

Entry
Database: PDB / ID: 5i1p
TitleVillin headpiece subdomain with a Lys30 to beta-3-homolysine substitution
Components
  • D-Villin headpiece subdomain
  • Villin-1
KeywordsDE NOVO PROTEIN / quasiracemic
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
ETHANOL / polypeptide(D) / polypeptide(D) (> 10) / Villin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsKreitler, D.F. / Mortenson, D.E. / Gellman, S.H. / Forest, K.T.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1518160 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM00839 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM061238 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM08293 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Effects of Single alpha-to-beta Residue Replacements on Structure and Stability in a Small Protein: Insights from Quasiracemic Crystallization.
Authors: Kreitler, D.F. / Mortenson, D.E. / Forest, K.T. / Gellman, S.H.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Refinement description
Revision 1.3Jul 13, 2016Group: Refinement description
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Villin-1
B: Villin-1
C: Villin-1
D: Villin-1
E: D-Villin headpiece subdomain
F: D-Villin headpiece subdomain
G: D-Villin headpiece subdomain
H: D-Villin headpiece subdomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,88011
Polymers32,7428
Non-polymers1383
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-14 kcal/mol
Surface area16230 Å2
Unit cell
Length a, b, c (Å)24.570, 40.600, 59.020
Angle α, β, γ (deg.)96.450, 90.660, 95.370
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
Villin-1


Mass: 4101.770 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide, fmoc solid phase synthesis / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P02640
#2: Polypeptide(D)
D-Villin headpiece subdomain


Mass: 4083.716 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide, fmoc solid phase synthesis / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.78 Å3/Da / Density % sol: 31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5, 20% (v/v) ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→40.16 Å / Num. obs: 42605 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 9.76
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.4-1.441.371.07193.3
1.44-1.481.1741.3193.6
1.48-1.520.8451.76193.9
1.52-1.570.6352.3194.4
1.57-1.620.5532.62194.8
1.62-1.670.4413.21195
1.67-1.740.3274.1195.4
1.74-1.810.2455.27195.6
1.81-1.890.1876.69196
1.89-1.980.1368.76196.5
1.98-2.090.09711.44196.6
2.09-2.210.07414.4197.3
2.21-2.370.06117.11197.5
2.37-2.560.05319.68197.7
2.56-2.80.04821.6197.9
2.8-3.130.04324.47198.3
3.13-3.610.03528.26198.6
3.61-4.430.03231.73199.1
4.43-6.260.0330.9199.3
6.260.03231.52196.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TRY

3try


Resolution: 1.4→40.16 Å / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.21 / Cross valid method: FREE R-VALUE
Displacement parametersBiso max: 76.49 Å2 / Biso mean: 29.6654 Å2 / Biso min: 12.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 9 151 2438

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