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- PDB-3nkj: Crystal Structure of HP67 L61G -

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Basic information

Entry
Database: PDB / ID: 3nkj
TitleCrystal Structure of HP67 L61G
ComponentsVillin-1
KeywordsSTRUCTURAL PROTEIN / Villin / Headpiece / Protein / Alpha Helix / Protein Folding
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 / positive regulation of actin filament bundle assembly / filopodium tip / actin filament severing / regulation of wound healing / actin filament capping / barbed-end actin filament capping ...regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / positive regulation of actin filament bundle assembly / filopodium tip / actin filament severing / regulation of wound healing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / 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 Domain; Chain A / Villin headpiece domain / 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 ...Villin Headpiece Domain; Chain A / Villin headpiece domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBrown, J.W. / Farelli, J.D. / McKnight, C.J.
CitationJournal: To be Published
Title: Conserving the Hydrophobic Core at the Expense of Backbone Conformation in Villin Headpiece
Authors: Brown, J.W. / Farelli, J.D. / McKnight, C.J.
History
DepositionJun 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)7,5561
Polymers7,5561
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.041, 39.544, 51.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Villin-1 /


Mass: 7555.556 Da / Num. of mol.: 1 / Fragment: Villin Headpiece (UNP Residues 760-826) / Mutation: L811G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: VIL1, VIL / Plasmid: pET-24A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02640
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M SODIUM ACETATE, 0.1 M CACODYLATE, 30% POLYETHYLENE GLYCOL 10,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→13.8943 Å / Num. obs: 7740 / % possible obs: 91.14 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.042
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.126 / Num. unique all: 1146 / % possible all: 83

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YU5

1yu5


Resolution: 1.6→13.894 Å / SU ML: 0.18 / σ(F): 0.22 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2186 779 10.06 %
Rwork0.1817 --
obs0.1854 7740 91.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.517 Å2 / ksol: 0.428 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1468 Å20 Å2-0 Å2
2--1.2643 Å2-0 Å2
3----1.4111 Å2
Refinement stepCycle: LAST / Resolution: 1.6→13.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms509 0 0 132 641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006520
X-RAY DIFFRACTIONf_angle_d1.101701
X-RAY DIFFRACTIONf_dihedral_angle_d12.893196
X-RAY DIFFRACTIONf_chiral_restr0.08475
X-RAY DIFFRACTIONf_plane_restr0.00493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.70020.21881170.17011029X-RAY DIFFRACTION83
1.7002-1.83120.21191270.16521136X-RAY DIFFRACTION91
1.8312-2.0150.231320.16451174X-RAY DIFFRACTION93
2.015-2.30540.22261280.16761158X-RAY DIFFRACTION91
2.3054-2.90020.22641340.18611198X-RAY DIFFRACTION94
2.9002-13.89430.19431410.18291266X-RAY DIFFRACTION94

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