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- PDB-3rq9: Structure of Tsi2, a Tse2-immunity protein from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 3rq9
TitleStructure of Tsi2, a Tse2-immunity protein from Pseudomonas aeruginosa
ComponentsType VI secretion immunity protein
KeywordsTSE2-BINDING PROTEIN / immunity protein / type VI secretion / T6S / antitoxin
Function / homologyHelix Hairpins - #2500 / Tse2 immunity protein Tsi2 / : / : / T6SS, Immune protein Tsi2-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Immune protein Tsi2
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1 Å
AuthorsLi, M. / Le Trong, I. / Stenkamp, R.E. / Mougous, J.D.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural Basis for Type VI Secretion Effector Recognition by a Cognate Immunity Protein.
Authors: Li, M. / Le Trong, I. / Carl, M.A. / Larson, E.T. / Chou, S. / De Leon, J.A. / Dove, S.L. / Stenkamp, R.E. / Mougous, J.D.
History
DepositionApr 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type VI secretion immunity protein
B: Type VI secretion immunity protein


Theoretical massNumber of molelcules
Total (without water)19,1912
Polymers19,1912
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-16 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.807, 34.063, 37.650
Angle α, β, γ (deg.)110.48, 95.94, 95.82
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Type VI secretion immunity protein / Tsi2


Mass: 9595.624 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2703 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9I0D9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 1.71 Å3/Da / Density % sol: 28.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8% PEG 4000, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9792, 0.9075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2009
RadiationMonochromator: double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.90751
ReflectionResolution: 0.99→50 Å / Num. all: 60521 / Num. obs: 60521 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 31.2
Reflection shellResolution: 0.99→1.01 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 3.7 / % possible all: 45

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0096refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1→34.88 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.701 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17613 3246 5.1 %RANDOM
Rwork0.14496 ---
obs0.14655 60525 91.24 %-
all-60521 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.31 Å2-0.08 Å2
2--0.4 Å2-0.02 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 0 175 1446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211388
X-RAY DIFFRACTIONr_bond_other_d0.0010.02907
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9531882
X-RAY DIFFRACTIONr_angle_other_deg1.02232255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0295165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87926.27986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.886158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
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_it3.074842
X-RAY DIFFRACTIONr_mcbond_other1.1684324
X-RAY DIFFRACTIONr_mcangle_it4.41161364
X-RAY DIFFRACTIONr_scbond_it5.8966556
X-RAY DIFFRACTIONr_scangle_it7.95810541
X-RAY DIFFRACTIONr_rigid_bond_restr3.45637119
X-RAY DIFFRACTIONr_sphericity_free11.5855188
X-RAY DIFFRACTIONr_sphericity_bonded7.61652270
LS refinement shellResolution: 0.995→1.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 176 -
Rwork0.215 3556 -
obs--72.19 %

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