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- PDB-3try: Crystal structure of racemic villin headpiece subdomain in space ... -

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Basic information

Entry
Database: PDB / ID: 3try
TitleCrystal structure of racemic villin headpiece subdomain in space group I-4c2
ComponentsD-Villin-1
KeywordsSTRUCTURAL PROTEIN / racemate
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 / barbed-end 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 / 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 / lamellipodium / actin cytoskeleton / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMortenson, D.E. / Satyshur, K.A. / Gellman, S.H. / Forest, K.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Quasiracemic crystallization as a tool to assess the accommodation of noncanonical residues in nativelike protein conformations.
Authors: Mortenson, D.E. / Satyshur, K.A. / Guzei, I.A. / Forest, K.T. / Gellman, S.H.
History
DepositionSep 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-Villin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1802
Polymers4,0841
Non-polymers961
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.128, 63.128, 39.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number120
Space group name H-MI-4c2

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Components

#1: Protein/peptide D-Villin-1


Mass: 4083.716 Da / Num. of mol.: 1 / Fragment: headpiece subdomain (UNP residues 792-826) / Mutation: N818H / Source method: obtained synthetically / Details: synthesized using Fmoc-protected D-amino acids / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P02640
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 298 K / pH: 5.75
Details: 2.0 M ammonium sulfate, 6% isopropanol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Apr 18, 2011
RadiationMonochromator: BRUKER MICROSTAR AXS OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→22.319 Å / Num. all: 1824 / Num. obs: 1772 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 17.58 % / Rsym value: 0.1259 / Net I/σ(I): 16.39
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 16.21 % / Mean I/σ(I) obs: 8.58 / Rsym value: 0.3122 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SAINTV7.68Adata reduction
REFMACrefinement
PDB_EXTRACT3.1data extraction
PROTEUM PLUSPLUSdata reduction
SAINTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YRF

1yrf


Resolution: 2.3→22.319 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.248 / SU ML: 0.119 / SU R Cruickshank DPI: 0.3166 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23006 79 4.5 %RANDOM
Rwork0.20047 ---
obs0.20186 1694 97.04 %-
all-1824 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.909 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.3→22.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms277 0 5 3 285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019287
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.752.579383
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.718533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07524.61513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.171151
X-RAY DIFFRACTIONr_chiral_restr0.1070.239
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021206
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4121.5168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8512265
X-RAY DIFFRACTIONr_scbond_it1.3853119
X-RAY DIFFRACTIONr_scangle_it2.4724.5118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.572 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.262 16 -
Rwork0.267 474 -
obs--96.46 %

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