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- PDB-3fg7: The crystal structure of villin domain 6 -

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Basic information

Entry
Database: PDB / ID: 3fg7
TitleThe crystal structure of villin domain 6
ComponentsVillin-1
KeywordsSTRUCTURAL PROTEIN / actin binding protein / Villin head piece / villin / gelsolin / Actin capping / Actin-binding / Calcium / Cytoplasm / Cytoskeleton
Function / homology
Function and homology information


terminal web assembly / intestinal D-glucose absorption / regulation of microvillus length / regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / positive regulation of actin filament depolymerization / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of lamellipodium morphogenesis ...terminal web assembly / intestinal D-glucose absorption / regulation of microvillus length / regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / positive regulation of actin filament depolymerization / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of lamellipodium morphogenesis / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / barbed-end actin filament capping / positive regulation of multicellular organism growth / actin polymerization or depolymerization / actin filament depolymerization / cellular response to hepatocyte growth factor stimulus / positive regulation of epithelial cell migration / actin filament bundle / microvillus / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / brush border / cellular response to epidermal growth factor stimulus / ruffle / epithelial cell differentiation / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / filopodium / positive regulation of protein localization to plasma membrane / response to bacterium / epidermal growth factor receptor signaling pathway / actin filament binding / actin cytoskeleton / lamellipodium / regulation of cell shape / protein-containing complex assembly / positive regulation of cell migration / apoptotic process / calcium ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / plasma membrane / 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 / Severin / Severin ...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 / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWang, H. / Burtnick, L.D. / Robinson, R.C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Helix-straightening as an activation mechanism in the gelsolin superfamily of actin regulatory proteins
Authors: Wang, H. / Chumnarnsilpa, S. / Loonchanta, A. / Li, Q. / Kuan, Y.M. / Robine, S. / Larsson, M. / Mihalek, I. / Burtnick, L.D. / Robinson, R.C.
History
DepositionDec 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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

Downloads & links

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Assembly

Deposited unit
A: Villin-1
B: Villin-1


Theoretical massNumber of molelcules
Total (without water)89,9632
Polymers89,9632
Non-polymers00
Water2,882160
1
A: Villin-1


Theoretical massNumber of molelcules
Total (without water)44,9821
Polymers44,9821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Villin-1


Theoretical massNumber of molelcules
Total (without water)44,9821
Polymers44,9821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.820, 47.820, 98.173
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21A
12G
22A
13G
23A
14G
24A
15G
25A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111G635 - 645
2111A635 - 645
1121G655 - 698
2121A655 - 698
1131G714 - 741
2131A714 - 741
1144G646 - 654
2144A646 - 654
1154G699 - 713
2154A699 - 713

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein Villin-1 /


Mass: 44981.551 Da / Num. of mol.: 2 / Fragment: Gelsolin-like repeats 4, 5, and 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VIL, VIL1 / Plasmid: pSY5 / Production host: Escherichia coli (E. coli) / References: UniProt: P09327
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: The protein(10mg/ml)was mixed in a 1:1 ratio(v/v)with a reservoir solution containing 15%(w/v)PEG8000, 100mM NaOAc buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 4.8 % / Av σ(I) over netI: 44.8 / Number: 80501 / Rmerge(I) obs: 0.048 / Χ2: 1.71 / D res high: 2 Å / D res low: 30 Å / Num. obs: 16865 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.313098.310.0372.8524.7
3.424.3199.210.0433.2524.8
2.993.4299.610.0412.2274.9
2.712.9999.910.0511.6655
2.522.7110010.0711.5225
2.372.5210010.0831.1635
2.252.3710010.1011.1155
2.152.2599.910.1581.1055
2.072.1510010.2241.0094.8
22.0798.810.2821.113.5
ReflectionResolution: 2→30 Å / Num. obs: 16865 / % possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.048
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.282 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.91 Å
Translation2.5 Å23.91 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1P8X

1p8x


Resolution: 2→23.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.303 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24622 807 4.8 %RANDOM
Rwork0.19727 ---
obs0.19961 16008 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.799 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→23.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 0 160 1910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221810
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9232472
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1292596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57815280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.688156
X-RAY DIFFRACTIONr_chiral_restr0.1350.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021428
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2807
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21180
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6831.51087
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.80721734
X-RAY DIFFRACTIONr_scbond_it3.1793841
X-RAY DIFFRACTIONr_scangle_it5.3024.5738
X-RAY DIFFRACTIONr_rigid_bond_restr2.29931928
X-RAY DIFFRACTIONr_sphericity_free4.4663160
X-RAY DIFFRACTIONr_sphericity_bonded1.43131750
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
190tight positional0.010.05
2366tight positional0.010.05
3229tight positional0.010.05
469medium positional0.20.5
5121medium positional0.160.5
190tight thermal0.150.5
2366tight thermal0.140.5
3229tight thermal0.130.5
469medium thermal0.142
5121medium thermal0.192
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 64 -
Rwork0.222 1147 -
obs--98.7 %

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