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- PDB-4noo: Molecular mechanism for self-protection against type VI secretion... -

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Basic information

Entry
Database: PDB / ID: 4noo
TitleMolecular mechanism for self-protection against type VI secretion system in Vibrio cholerae
Components
  • Putative uncharacterized protein
  • VgrG protein
KeywordsIMMUNE SYSTEM / self-protection / chitosanase-fold / three-helical bundle / glycoside hydrolase effector / immunity protein
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity / extracellular region / identical protein binding
Similarity search - Function
: / Type VI secretion system spike protein VgrG3-like, C-terminal / Helicase, Ruva Protein; domain 3 - #1160 / : / : / Antitoxin TsiV3 / Bacteriophage T4 gp5 C-terminal trimerisation domain / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / Phage tail baseplate hub (GPD) ...: / Type VI secretion system spike protein VgrG3-like, C-terminal / Helicase, Ruva Protein; domain 3 - #1160 / : / : / Antitoxin TsiV3 / Bacteriophage T4 gp5 C-terminal trimerisation domain / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / PGBD superfamily / Vgr protein, OB-fold domain superfamily / : / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Antitoxin protein TsiV3 / Type VI secretion system spike protein VgrG3
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsYang, X. / Xu, M. / Jiang, T. / Fan, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Molecular mechanism for self-protection against the type VI secretion system in Vibrio cholerae.
Authors: Yang, X. / Xu, M. / Wang, Y. / Xia, P. / Wang, S. / Ye, B. / Tong, L. / Jiang, T. / Fan, Z.
History
DepositionNov 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VgrG protein
B: Putative uncharacterized protein
C: VgrG protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)69,8694
Polymers69,8694
Non-polymers00
Water9,458525
1
A: VgrG protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)34,9342
Polymers34,9342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-12 kcal/mol
Surface area14960 Å2
MethodPISA
2
C: VgrG protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)34,9342
Polymers34,9342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-12 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.502, 116.034, 68.225
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VgrG protein


Mass: 23576.129 Da / Num. of mol.: 2 / Fragment: VgrG3C catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0123 / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: Q9KN42
#2: Protein Putative uncharacterized protein


Mass: 11358.249 Da / Num. of mol.: 2
Fragment: TsiV3 without the predicted 24aa N-terminal periplasm localization signal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0124 / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: Q9KN41
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% (m/v) PEG8000, 0.1M Sodium Cacodylate pH5.6, 0.2M Mg acetate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9789 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 11, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→29.5 Å / Num. all: 34369 / Num. obs: 34369 / % possible obs: 99.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 28
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.5 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23441 1822 5 %RANDOM
Rwork0.18629 ---
obs0.18868 34369 99.92 %-
all-34369 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-0.05 Å2
2---1.13 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4734 0 0 525 5259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194830
X-RAY DIFFRACTIONr_bond_other_d00.024546
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9516508
X-RAY DIFFRACTIONr_angle_other_deg3.5973.00210454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3895586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74725.041246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6715842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6321524
X-RAY DIFFRACTIONr_chiral_restr0.0740.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025542
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021158
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 115 -
Rwork0.233 2539 -
obs--99.66 %

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