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- PDB-4hzb: Crystal structure of the type VI SeMet effector-immunity complex ... -

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Basic information

Entry
Database: PDB / ID: 4hzb
TitleCrystal structure of the type VI SeMet effector-immunity complex Tae3-Tai3 from Ralstonia pickettii
Components
  • Putative cytoplasmic proteinCytoplasm
  • Putative periplasmic proteinPeriplasm
KeywordsHYDROLASE / protein-protein complex / alpha+beta / endopeptidase / periplasmic space
Function / homology
Function and homology information


Domain of unknown function DUF3828 / Protein of unknown function (DUF3828) / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Putative cytoplasmic protein / Putative periplasmic protein
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsDong, C. / Zhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Biochem.J. / Year: 2013
Title: Structural insights into the inhibition of type VI effector Tae3 by its immunity protein Tai3
Authors: Dong, C. / Zhang, H. / Gao, Z.Q. / Wang, W.J. / She, Z. / Liu, G.F. / Shen, Y.Q. / Su, X.D. / Dong, Y.H.
History
DepositionNov 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cytoplasmic protein
B: Putative periplasmic protein
C: Putative periplasmic protein
D: Putative cytoplasmic protein
E: Putative periplasmic protein
F: Putative periplasmic protein


Theoretical massNumber of molelcules
Total (without water)95,7306
Polymers95,7306
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-29 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.199, 126.943, 143.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative cytoplasmic protein / Cytoplasm / toxin protein


Mass: 13241.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: 12D / Gene: Rpic12D_3261 / Production host: Escherichia coli (E. coli) / References: UniProt: C6BHF2
#2: Protein
Putative periplasmic protein / Periplasm / antitoxin protein


Mass: 17311.689 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: 12D / Gene: Rpic12D_3260 / Production host: Escherichia coli (E. coli) / References: UniProt: C6BHF3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.01M ferric chloride hexahydrate, 0.1M tri-sodium citrate dihydrate pH5.6, 10% v/v jeffamine M-600 , pH 5.6 , VAPOR DIFFUSION, SITTING DROP, temperature 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 32353 / Num. obs: 32299 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 27.08 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 24.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1529 / % possible all: 96

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→35.054 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8081 / SU ML: 0.38 / σ(F): 5.59 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2706 1999 6.19 %random
Rwork0.2159 ---
all0.2194 32353 --
obs0.2159 32299 99.34 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.065 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 97.77 Å2 / Biso mean: 28.4819 Å2 / Biso min: 6.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.4179 Å20 Å20 Å2
2--0.4622 Å20 Å2
3----0.0443 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5655 0 0 161 5816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095831
X-RAY DIFFRACTIONf_angle_d1.1777955
X-RAY DIFFRACTIONf_dihedral_angle_d14.882065
X-RAY DIFFRACTIONf_chiral_restr0.08833
X-RAY DIFFRACTIONf_plane_restr0.0061030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5997-2.66470.31781340.2579202192
2.6647-2.73670.3281370.26172097100
2.7367-2.81720.31361430.25022160100
2.8172-2.90810.30281400.23612111100
2.9081-3.0120.32531410.24432145100
3.012-3.13250.32461420.24882162100
3.1325-3.2750.30561430.23932158100
3.275-3.44750.29311420.2312147100
3.4475-3.66330.27051430.21772162100
3.6633-3.94580.24971430.20292176100
3.9458-4.34220.25681450.18842200100
4.3422-4.9690.20621450.17022190100
4.969-6.25470.23211470.19482241100
6.2547-35.05680.23571540.2025233099

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