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- PDB-3ryl: Dimerization domain of Vibrio parahemolyticus VopL -

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Basic information

Entry
Database: PDB / ID: 3ryl
TitleDimerization domain of Vibrio parahemolyticus VopL
Componentsprotein VPA1370
KeywordsPROTEIN BINDING / Actin nucleation / Filament pointed end binding / Type III Secretion System (T3SS) protein
Function / homology
Function and homology information


actin binding / identical protein binding
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1210 / : / : / VopL C-terminal dimerization domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / WH2 domain / WH2 domain profile. ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1210 / : / : / VopL C-terminal dimerization domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / WH2 domain / WH2 domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
WH2 domain-containing protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsNamgoong, S. / Dominguez, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Mechanism of actin filament nucleation by Vibrio VopL and implications for tandem W domain nucleation.
Authors: Namgoong, S. / Boczkowska, M. / Glista, M.J. / Winkelman, J.D. / Rebowski, G. / Kovar, D.R. / Dominguez, R.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein VPA1370
B: protein VPA1370


Theoretical massNumber of molelcules
Total (without water)54,1292
Polymers54,1292
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-15 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.930, 90.490, 101.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein protein VPA1370 / actin filament pointed end-binding domain


Mass: 27064.623 Da / Num. of mol.: 2 / Fragment: VopL dimerization domain (UNP residues 247-484)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VopL, VPA1370 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87GE5

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13-15% PEG3350, 0.2 M sodium fluoride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9772
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 29, 2011 / Details: Bent, triangular Si(111) monochromator crystal
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 3.1→67.65 Å / Num. all: 10025 / Num. obs: 10025 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 32.75 % / Biso Wilson estimate: 107.97 Å2 / Rmerge(I) obs: 0.1224 / Rsym value: 0.1224 / Net I/σ(I): 20.56
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 34.86 % / Rmerge(I) obs: 0.4257 / Mean I/σ(I) obs: 2.37 / Num. unique all: 897 / Rsym value: 0.4257 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→67.65 Å / SU ML: 0.57 / σ(F): 0 / σ(I): 0 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2936 975 9.98 %RANDOM
Rwork0.2403 ---
all0.2459 9773 --
obs0.2459 9773 97.41 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 118.768 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 149.12 Å2
Baniso -1Baniso -2Baniso -3
1-4.9409 Å20 Å2-0 Å2
2--6.7217 Å20 Å2
3----11.428 Å2
Refinement stepCycle: LAST / Resolution: 3.1→67.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 0 0 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073534
X-RAY DIFFRACTIONf_angle_d1.5124750
X-RAY DIFFRACTIONf_dihedral_angle_d16.6091322
X-RAY DIFFRACTIONf_chiral_restr0.101527
X-RAY DIFFRACTIONf_plane_restr0.005620
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.1003-3.26380.37111190.31631131125090
3.2638-3.46820.39331380.2971215135396
3.4682-3.7360.29631370.29831235137298
3.736-4.11190.27791430.24321273141699
4.1119-4.70680.2751420.213412791421100
4.7068-5.92950.31541440.256613051449100
5.9295-67.66640.27671520.21481360151299

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