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- PDB-3tjw: Crystal Structure of Quasiracemic Villin Headpiece Subdomain Cont... -

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Basic information

Entry
Database: PDB / ID: 3tjw
TitleCrystal Structure of Quasiracemic Villin Headpiece Subdomain Containing (F5Phe10) Substitution
Components
  • D-Villin-1
  • L-Villin-1
KeywordsSTRUCTURAL PROTEIN / pentafluorophenylalanine
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
polypeptide(D) / polypeptide(D) (> 10) / Villin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 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
DepositionAug 25, 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 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-Villin-1
B: L-Villin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2565
Polymers7,9682
Non-polymers2883
Water1,17165
1
A: D-Villin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1293
Polymers3,9371
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-Villin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1282
Polymers4,0321
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.656, 88.112, 88.663
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Polypeptide(D) D-Villin-1


Mass: 3936.542 Da / Num. of mol.: 1 / Fragment: headpiece subdomain (UNP residues 792-825) / Mutation: N818H / Source method: obtained synthetically / Details: synthesized using Fmoc-protected D-amino acids / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P02640
#2: Protein/peptide L-Villin-1


Mass: 4031.529 Da / Num. of mol.: 1 / Fragment: headpiece subdomain (UNP residues 792-825) / Mutation: N818H / Source method: obtained synthetically / Details: synthesized using Fmoc-protected L-amino acids / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P02640
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
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 298.0K

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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: Oct 17, 2010
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.46→32.88 Å / Num. all: 13191 / Num. obs: 13191 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.4 % / Rsym value: 0.034 / Χ2: 0.956 / Net I/σ(I): 34.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueΧ2Diffraction-ID% possible all
1.46-1.49135690.081.08186.2
1.49-1.5114.56460.071.0641100
1.51-1.5414.66580.0621.0691100
1.54-1.5714.56580.0541.0861100
1.57-1.6114.66760.0460.9631100
1.61-1.6414.56420.0450.9521100
1.64-1.6914.76580.0381.0051100
1.69-1.7314.66690.0350.9751100
1.73-1.7814.66710.0340.9741100
1.78-1.8414.76650.0320.8961100
1.84-1.9114.76430.030.8921100
1.91-1.9814.66680.0290.921100
1.98-2.0714.76650.0260.8521100
2.07-2.1814.66640.0271.1521100
2.18-2.3214.66710.0310.8381100
2.32-2.514.76720.040.9171100
2.5-2.7514.66770.0530.9631100
2.75-3.1514.66800.050.837199.7
3.15-3.9613.66830.0260.72198.3
3.96-5012.26560.021.001190.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.88 Å
Translation2.5 Å32.88 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MD2EMBLdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→32.88 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2241 / WRfactor Rwork: 0.1686 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8926 / SU B: 1.825 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0715 / SU Rfree: 0.0652 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 646 4.9 %RANDOM
Rwork0.1501 ---
obs0.1521 13190 98.7 %-
all-13191 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.63 Å2 / Biso mean: 15.3321 Å2 / Biso min: 7.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0 Å2
2--0.16 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.46→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms559 0 15 65 639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021615
X-RAY DIFFRACTIONr_bond_other_d0.0040.02443
X-RAY DIFFRACTIONr_angle_refined_deg1.7332.3827
X-RAY DIFFRACTIONr_angle_other_deg0.8263.0021075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.386572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.31323.84613
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.971559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.399152
X-RAY DIFFRACTIONr_chiral_restr0.0770.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02133
X-RAY DIFFRACTIONr_rigid_bond_restr1.931058
X-RAY DIFFRACTIONr_sphericity_free38.429529
X-RAY DIFFRACTIONr_sphericity_bonded8.18451081
LS refinement shellResolution: 1.47→1.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.159 41 -
Rwork0.122 869 -
all-910 -
obs--100 %

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