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- PDB-3mya: Crystal Structure of HP67 H41F - P61 -

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Basic information

Entry
Database: PDB / ID: 3mya
TitleCrystal Structure of HP67 H41F - P61
ComponentsVillin-1
KeywordsSTRUCTURAL PROTEIN / villin headpiece / alpha helix / protein
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: 2.5 Å
AuthorsBrown, J.W. / Farelli, J.D. / McKnight, C.J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: On unsatisfied hydrogen bonds in the N-terminal subdomain of villin headpiece.
Authors: Brown, J.W. / Farelli, J.D. / McKnight, C.J.
History
DepositionMay 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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
B: Villin-1


Theoretical massNumber of molelcules
Total (without water)15,2412
Polymers15,2412
Non-polymers00
Water50428
1
A: Villin-1


Theoretical massNumber of molelcules
Total (without water)7,6211
Polymers7,6211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Villin-1


Theoretical massNumber of molelcules
Total (without water)7,6211
Polymers7,6211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.409, 65.409, 68.283
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Villin-1 /


Mass: 7620.689 Da / Num. of mol.: 2 / Fragment: Villin Headpiece (unp residues 760-826) / Mutation: H41F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: VIL, VIL1 / 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.: 28 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium Sulfate, 0.1 M 2-morpholinoethanesulfonic Acid, 30% Polyethylene Glycol 8,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→18.9 Å / Num. all: 5704 / Num. obs: 5554 / % possible obs: 95.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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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 2RJW

2rjw


Resolution: 2.5→18.9 Å / SU ML: 0.34 / σ(F): -3 / σ(I): 5.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 256 4.61 %RANDOM
Rwork0.2147 ---
obs0.2175 5554 95.92 %-
all-5704 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.576 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1369 Å2-0 Å2-0 Å2
2--3.1369 Å2-0 Å2
3----6.2739 Å2
Refinement stepCycle: LAST / Resolution: 2.5→18.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 0 28 1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081076
X-RAY DIFFRACTIONf_angle_d1.0061452
X-RAY DIFFRACTIONf_dihedral_angle_d14.262409
X-RAY DIFFRACTIONf_chiral_restr0.069158
X-RAY DIFFRACTIONf_plane_restr0.004191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-3.14740.35591250.2642628X-RAY DIFFRACTION95
3.1474-18.88250.23891310.19132670X-RAY DIFFRACTION97

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