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- PDB-6itw: Crystal structure of Atu4351 from Agrobacterium tumefaciens -

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Basic information

Entry
Database: PDB / ID: 6itw
TitleCrystal structure of Atu4351 from Agrobacterium tumefaciens
ComponentsType VI immunity protein Atu4351
KeywordsANTITOXIN / type six secretion system / effector-immunity pair / Tdi1 / GAD-like domain / DUF1851 domain
Function / homologyGAD-related / T6SS immunity protein Tdi1, C-terminal / GAD-like domain / T6SS immunity protein Tdi1, C-terminal / GAD-related domain-containing protein
Function and homology information
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsShi, L. / Gao, Z. / Zhang, H. / Dong, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670059 China
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Crystal structure of the type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens.
Authors: Shi, L. / Gao, Z. / Zhang, T. / Zhang, H. / Dong, Y.
History
DepositionNov 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type VI immunity protein Atu4351


Theoretical massNumber of molelcules
Total (without water)26,3571
Polymers26,3571
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.445, 92.445, 86.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-380-

HOH

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Components

#1: Protein Type VI immunity protein Atu4351


Mass: 26357.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: Atu4351 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CUQ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.6 Å3/Da / Density % sol: 65.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium (pH7.5), 2%(v/v) PEG400, 2 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 8, 2015
RadiationProtocol: 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: 16565 / % possible obs: 96.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.056 / Net I/σ(I): 15.1
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 682 / Rrim(I) all: 0.57 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→31.514 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.82
RfactorNum. reflection% reflection
Rfree0.2496 1466 10.08 %
Rwork0.2153 --
obs0.2188 14540 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→31.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 0 80 1815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081790
X-RAY DIFFRACTIONf_angle_d0.9562423
X-RAY DIFFRACTIONf_dihedral_angle_d12.2181087
X-RAY DIFFRACTIONf_chiral_restr0.052264
X-RAY DIFFRACTIONf_plane_restr0.005316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3998-2.48560.36291440.2661174X-RAY DIFFRACTION89
2.4856-2.5850.28321440.23521215X-RAY DIFFRACTION92
2.585-2.70260.34131150.27451246X-RAY DIFFRACTION92
2.7026-2.8450.30721420.2561275X-RAY DIFFRACTION95
2.845-3.02310.28951580.26221314X-RAY DIFFRACTION99
3.0231-3.25630.29271550.26521322X-RAY DIFFRACTION99
3.2563-3.58360.26631490.2131323X-RAY DIFFRACTION97
3.5836-4.10120.22711490.19121335X-RAY DIFFRACTION98
4.1012-5.16340.1631530.16351381X-RAY DIFFRACTION100
5.1634-31.51670.24081570.211489X-RAY DIFFRACTION100

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