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- PDB-5i1n: Villin headpiece subdomain with a Gln26 to beta-3-homoglutamine s... -

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Basic information

Entry
Database: PDB / ID: 5i1n
TitleVillin headpiece subdomain with a Gln26 to beta-3-homoglutamine substitution
Components
  • D-Villin headpiece subdomain
  • Villin-1
KeywordsDE NOVO PROTEIN / quasiracemic / foldamer / alpha/beta peptide
Function / homology
Function and homology information


regulation of actin nucleation / lysophosphatidic acid binding / cytoplasmic actin-based contraction involved in cell motility / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / barbed-end actin filament capping / actin filament depolymerization ...regulation of actin nucleation / lysophosphatidic acid binding / cytoplasmic actin-based contraction involved in cell motility / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / barbed-end actin filament capping / actin filament depolymerization / actin filament capping / actin polymerization or depolymerization / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cellular response to hepatocyte growth factor stimulus / actin filament bundle / microvillus / positive regulation of epithelial cell migration / ruffle / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / cellular response to epidermal growth factor stimulus / filopodium / response to bacterium / epidermal growth factor receptor signaling pathway / actin filament binding / regulation of cell shape / lamellipodium / actin cytoskeleton / 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
polypeptide(D) / polypeptide(D) (> 10) / Villin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKreitler, D.F. / Mortenson, D.E. / Gellman, S.H. / Forest, K.T.
Funding support United States, 4items
OrganizationGrant numberCountry
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)T32GM08293 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM00839 United States
National Science Foundation (NSF, United States)MCB 1518160 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 1.2Jul 13, 2016Group: Refinement description
Revision 1.3Sep 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 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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_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


Theoretical massNumber of molelcules
Total (without water)32,7468
Polymers32,7468
Non-polymers00
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-36 kcal/mol
Surface area15290 Å2
Unit cell
Length a, b, c (Å)36.390, 38.860, 48.370
Angle α, β, γ (deg.)101.090, 110.500, 99.350
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
Villin-1


Mass: 4102.778 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 1.86 Å3/Da / Density % sol: 34 % / Description: plate-like
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 1.5 M ammonium sulfate, 30% (v/v) PEG2000MME

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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: 1.3→36.92 Å / Num. obs: 53932 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.591 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.09 / Χ2: 0.989 / Net I/σ(I): 8.73 / Num. measured all: 210950
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.331.8650.6911627425330170.3842.16570.9
1.33-1.371.5450.8714806418537860.4261.79190.5
1.37-1.411.1111.2515056409838010.5471.28592.8
1.41-1.450.9651.4314626395536860.7071.11693.2
1.45-1.50.6322.2114266383935950.8520.7393.6
1.5-1.550.522.6313840371234880.8990.60194
1.55-1.610.3863.4713329356033570.9340.44694.3
1.61-1.680.3194.0413024346532740.9570.36994.5
1.68-1.750.2265.6912446330531470.9750.26295.2
1.75-1.840.1757.1311925315430050.9850.20295.3
1.84-1.940.1369.1611220301328580.990.15794.9
1.94-2.060.0951210654285927170.9950.11195
2.06-2.20.06915.4810029265125510.9970.07996.2
2.2-2.370.05718.29255248023960.9970.06696.6
2.37-2.60.04920.448413232522140.9980.05795.2
2.6-2.910.04422.667709204119870.9980.0597.4
2.91-3.360.0425.296702182217800.9980.04697.7
3.36-4.110.03528.85359154914890.9980.04196.1
4.11-5.810.03130.574338118311570.9980.03697.8
5.810.02930.0323266596270.9990.03495.1

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Processing

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

3try


Resolution: 1.3→36.92 Å / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.206 / Cross valid method: FREE R-VALUE
Displacement parametersBiso max: 107.37 Å2 / Biso mean: 25.1688 Å2 / Biso min: 7.89 Å2
Refinement stepCycle: LAST / Resolution: 1.3→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 0 310 2622

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