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- PDB-3trw: Crystal structure of racemic villin headpiece subdomain crystalli... -

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Basic information

Entry
Database: PDB / ID: 3trw
TitleCrystal structure of racemic villin headpiece subdomain crystallized in space group P-1
ComponentsVillin-1
KeywordsSTRUCTURAL PROTEIN / racemate / quasi-racemate / D-amino acids
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 / 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 / actin filament capping / actin filament depolymerization / barbed-end actin filament capping / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 / 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
D: Villin-1


Theoretical massNumber of molelcules
Total (without water)7,9472
Polymers7,9472
Non-polymers00
Water34219
1
A: Villin-1


Theoretical massNumber of molelcules
Total (without water)3,9741
Polymers3,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Villin-1


Theoretical massNumber of molelcules
Total (without water)3,9741
Polymers3,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.3800, 31.7300, 36.7500
Angle α, β, γ (deg.)90.1170, 99.6140, 96.5210
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein/peptide Villin-1


Mass: 3973.618 Da / Num. of mol.: 2 / Fragment: headpiece subdomain (UNP residues 792-826) / Mutation: N818H / Source method: obtained synthetically / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P02640
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.04 Å3/Da / Density % sol: 39.68 % / Description: STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 2.0 M ammonium sulfate, 6% isopropanol, 8% glycerol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Aug 20, 2010
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionNumber: 31416 / Rmerge(I) obs: 0.084 / D res high: 2 Å / Num. obs: 8212 / % possible obs: 96.7
Diffraction reflection shellHighest resolution: 4.31 Å / Lowest resolution: 5.42 Å / Num. obs: 421 / % possible obs: 98.6 % / Rmerge(I) obs: 0.064
ReflectionResolution: 2.1→27.794 Å / Num. all: 7334 / Num. obs: 7112 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.71 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.0772 / Net I/σ(I): 8.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. unique allNum. unique obsRsym value% possible all
2.1-2.133.743.0214352203750.29697.3
2.13-2.183.683.6715534444050.253995.9
2.18-2.233.684.1616284364260.216995.8
2.23-2.283.764.514623763780.194796.7
2.28-2.343.734.8916884284430.17996.8
2.34-2.43.765.115553764010.174997.2
2.4-2.473.736.2416803974360.14596.8
2.47-2.553.726.4815294033960.147496.6
2.55-2.633.756.7315933684120.119896.8
2.63-2.733.737.2315843704110.120897.1
2.73-2.833.788.116153644170.103497.6
2.83-2.973.759.3914813723860.108796.6
2.97-3.133.7910.4717933794620.087597.9
3.13-3.333.7211.0314623743770.079697.4
3.33-3.593.612.7216293654230.068295.8
3.59-3.963.6114.8815433684050.064897.9
3.96-4.533.6215.3415003574030.059697.3
4.53-5.693.615.5815423574160.062497.8
5.693.7216.3415573584210.059797.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å27.79 Å
Translation3 Å27.79 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
EMBLMD-2data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YRF

1yrf


Resolution: 2.1→27.794 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.3887 / WRfactor Rwork: 0.3243 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.6649 / SU B: 12.808 / SU ML: 0.152 / SU R Cruickshank DPI: 0.2214 / SU Rfree: 0.2185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
RfactorNum. reflection% reflectionSelection details
Rfree0.3518 334 4.7 %RANDOM
Rwork0.2913 ---
obs0.2942 7112 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.55 Å2 / Biso mean: 34.9553 Å2 / Biso min: 19.39 Å2
Baniso -1Baniso -2Baniso -3
1-6.13 Å2-1.07 Å2-1.07 Å2
2---3.7 Å2-0.33 Å2
3----3.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.221 Å
Refinement stepCycle: LAST / Resolution: 2.1→27.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 0 19 555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022553
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.979735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.716568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90224.425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62715113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.387153
X-RAY DIFFRACTIONr_chiral_restr0.0880.279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021401
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree: 0.419 / Rfactor Rwork: 0.43 / Total num. of bins used: 20
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.67770.6452-1.6026.6231-3.71783.0390.151-0.1479-0.0762-0.3432-0.2131-0.0130.050.21830.06210.09140.0182-0.01780.0514-0.00260.00639.70735.6855.4935
20.5255-1.09180.7987.93322.83864.81760.0569-0.04450.0708-0.1588-0.139-0.12260.0492-0.26890.08220.0398-0.00090.00650.10030.00280.06712.02029.491124.6445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 34
2X-RAY DIFFRACTION2D1 - 34

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