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- PDB-4nso: Crystal structure of the effector-immunity protein complex -

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Basic information

Entry
Database: PDB / ID: 4nso
TitleCrystal structure of the effector-immunity protein complex
Components
  • Effector proteinEffector (biology)
  • Immunity protein
KeywordsPROTEIN BINDING / Helix / peptidoglycan
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 / Type VI secretion system, RhsGE-associated Vgr family subset / Phage tail baseplate hub (GPD) / Type VI secretion system, RhsGE-associated Vgr protein / Gp5/Type VI secretion system Vgr protein, OB-fold domain ...: / Type VI secretion system spike protein VgrG3-like, C-terminal / Helicase, Ruva Protein; domain 3 - #1160 / : / : / Antitoxin TsiV3 / Type VI secretion system, RhsGE-associated Vgr family subset / Phage tail baseplate hub (GPD) / 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 / PGBD 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: 2.4 Å
AuthorsDong, C.
CitationJournal: Febs Lett. / Year: 2014
Title: Structural basis for recognition of the type VI spike protein VgrG3 by a cognate immunity protein.
Authors: Zhang, J. / Zhang, H. / Gao, Z. / Hu, H. / Dong, C. / Dong, Y.H.
History
DepositionNov 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 11, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Effector protein
B: Immunity protein


Theoretical massNumber of molelcules
Total (without water)46,8422
Polymers46,8422
Non-polymers00
Water1,928107
1
A: Effector protein
B: Immunity protein

A: Effector protein
B: Immunity protein


Theoretical massNumber of molelcules
Total (without water)93,6844
Polymers93,6844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8290 Å2
ΔGint-30 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.631, 78.660, 47.860
Angle α, β, γ (deg.)90.00, 101.52, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x+1,y,-z+1

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Components

#1: Protein Effector protein / Effector (biology) / VgrG protein


Mass: 34151.254 Da / Num. of mol.: 1 / Fragment: UNP residues 731-981
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VCPCS023_003519, VC_A0123 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KN42
#2: Protein Immunity protein /


Mass: 12690.626 Da / Num. of mol.: 1 / Fragment: UNP residues 26-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC_A0124 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KN41
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1mM HEPES pH7.6, 12%(w/v)PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19076 / Redundancy: 7.5 % / Rmerge(I) obs: 0.073
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.9 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→38.165 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 27.75 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.259 1847 10 %
Rwork0.2155 --
obs0.2199 18466 96.76 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.437 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.4964 Å20 Å27.3188 Å2
2--10.023 Å20 Å2
3----0.5266 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 0 107 2450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092390
X-RAY DIFFRACTIONf_angle_d1.0483218
X-RAY DIFFRACTIONf_dihedral_angle_d14.828890
X-RAY DIFFRACTIONf_chiral_restr0.076343
X-RAY DIFFRACTIONf_plane_restr0.006415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46490.35761220.31041127X-RAY DIFFRACTION87
2.4649-2.53740.36331320.28371241X-RAY DIFFRACTION94
2.5374-2.61930.33061430.2681261X-RAY DIFFRACTION96
2.6193-2.71290.32651400.25051253X-RAY DIFFRACTION96
2.7129-2.82150.30721420.24571270X-RAY DIFFRACTION97
2.8215-2.94980.28891460.23881301X-RAY DIFFRACTION98
2.9498-3.10530.29191440.2211292X-RAY DIFFRACTION98
3.1053-3.29980.27541450.22661289X-RAY DIFFRACTION99
3.2998-3.55440.24191440.23081291X-RAY DIFFRACTION97
3.5544-3.91170.26831450.21611297X-RAY DIFFRACTION98
3.9117-4.4770.2091470.1711311X-RAY DIFFRACTION99
4.477-5.63770.20551480.17721330X-RAY DIFFRACTION99
5.6377-38.17010.24171490.20491356X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 42.9516 Å / Origin y: 47.797 Å / Origin z: 36.6877 Å
111213212223313233
T0.3119 Å2-0.0354 Å2-0.0265 Å2-0.31 Å20.0454 Å2--0.1917 Å2
L4.0665 °2-0.1037 °2-1.444 °2-0.8748 °20.0681 °2--1.8228 °2
S-0.1215 Å °0.2736 Å °-0.1459 Å °-0.0588 Å °0.1283 Å °0.1587 Å °0.1983 Å °-0.3371 Å °-0.0025 Å °
Refinement TLS groupSelection details: all

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