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- PDB-3wit: Crystal structure of the C-terminal region of VgrG1 from E. coli ... -

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Basic information

Entry
Database: PDB / ID: 3wit
TitleCrystal structure of the C-terminal region of VgrG1 from E. coli O157 EDL933
ComponentsPutative Vgr protein
KeywordsSTRUCTURAL PROTEIN / Triple-stranded beta-helix / All beta proteins / Type 6 secretion system component
Function / homology
Function and homology information


Glycosyl hydrolase fold - #20 / Glycosyl hydrolase fold / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Type VI secretion system Vgr family protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsUchida, K. / Leiman, P.G. / Arisaka, F. / Kanamaru, S.
CitationJournal: J.Biochem. / Year: 2014
Title: Structure and properties of the C-terminal beta-helical domain of VgrG protein from Escherichia coli O157
Authors: Uchida, K. / Leiman, P.G. / Arisaka, F. / Kanamaru, S.
History
DepositionSep 25, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Vgr protein


Theoretical massNumber of molelcules
Total (without water)8,6181
Polymers8,6181
Non-polymers00
Water23413
1
A: Putative Vgr protein

A: Putative Vgr protein

A: Putative Vgr protein


Theoretical massNumber of molelcules
Total (without water)25,8553
Polymers25,8553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6670 Å2
ΔGint-53 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.417, 49.417, 199.143
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Putative Vgr protein / Uncharacterized protein


Mass: 8618.481 Da / Num. of mol.: 1 / Fragment: UNP residues 561-633
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: ECs0607, VgrG1, Z0707 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): B384(DE3) / References: UniProt: Q8XBY5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 35%(v/v) ethanol, 100mM Tris pH8.5, 50mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 9, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.95→41.84 Å / Num. all: 7237 / Num. obs: 7223 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 18.3 % / Biso Wilson estimate: 32.45 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 43.1
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1026 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→33.191 Å / SU ML: 0.15 / Isotropic thermal model: Isotropic / σ(F): 0.08 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 326 4.64 %RANDOM
Rwork0.1961 ---
obs0.1978 7023 97.18 %-
all-7228 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms477 0 0 13 490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012483
X-RAY DIFFRACTIONf_angle_d1.654651
X-RAY DIFFRACTIONf_dihedral_angle_d17.841170
X-RAY DIFFRACTIONf_chiral_restr0.1281
X-RAY DIFFRACTIONf_plane_restr0.00681
LS refinement shellResolution: 1.95→2.4547 Å
RfactorNum. reflection% reflection
Rfree0.2452 151 -
Rwork0.1826 3213 -
obs-3213 95 %
Refinement TLS params.Method: refined / Origin x: 20.2795 Å / Origin y: 20.1684 Å / Origin z: 85.2587 Å
111213212223313233
T0.2357 Å20.0423 Å20.0047 Å2-0.2017 Å2-0.0265 Å2--0.3322 Å2
L2.583 °20.0288 °2-0.8271 °2-1.6787 °2-0.3416 °2--6.5166 °2
S-0.049 Å °-0.025 Å °0.224 Å °0.0661 Å °0.0194 Å °0.1568 Å °-0.5238 Å °-0.1961 Å °-0.0058 Å °
Refinement TLS groupSelection details: all

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