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- PDB-3vpv: Crystal Structure of Pseudomonas aeruginosa Tsi2 -

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Basic information

Entry
Database: PDB / ID: 3vpv
TitleCrystal Structure of Pseudomonas aeruginosa Tsi2
ComponentsTse2 specific immunity protein 2
KeywordsTOXIN INHIBITOR
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 / SAD / Resolution: 1.8 Å
AuthorsWang, W. / Ding, J. / Wang, D.C.
CitationJournal: To be Published
Title: Crystal Structure of Pseudomonas aeruginosa Tsi2
Authors: Wang, W. / Ding, J. / Wang, D.C.
History
DepositionMar 13, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tse2 specific immunity protein 2
B: Tse2 specific immunity protein 2


Theoretical massNumber of molelcules
Total (without water)19,3792
Polymers19,3792
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-16 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.380, 34.920, 38.490
Angle α, β, γ (deg.)110.37, 95.98, 95.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tse2 specific immunity protein 2


Mass: 9689.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA2703 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9I0D9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 1.82 Å3/Da / Density % sol: 32.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% PEG 3350, 0.1mM sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→19.794 Å / Num. all: 12278 / Num. obs: 12200 / % possible obs: 99.4 % / Redundancy: 4 % / Biso Wilson estimate: 16.878 Å2 / Rmerge(I) obs: 0.022 / Rsym value: 0.022 / Net I/σ(I): 36.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.047 / Mean I/σ(I) obs: 16 / Num. unique all: 1771 / Rsym value: 0.047 / % possible all: 95.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.794 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8631 / SU ML: 0.21 / σ(F): 0.08 / Phase error: 21.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 588 4.85 %Random
Rwork0.1847 ---
obs0.1862 12131 96 %-
all-12200 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.089 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso max: 43.61 Å2 / Biso mean: 16.23 Å2 / Biso min: 3.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.4448 Å21.317 Å21.6702 Å2
2--1.7431 Å21.8656 Å2
3----1.2983 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 0 218 1499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051303
X-RAY DIFFRACTIONf_angle_d0.7421775
X-RAY DIFFRACTIONf_dihedral_angle_d13.816491
X-RAY DIFFRACTIONf_chiral_restr0.05197
X-RAY DIFFRACTIONf_plane_restr0.004244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.9810.2561460.2178281994
1.981-2.26730.21331500.1835291196
2.2673-2.85530.23541380.1901289796
2.8553-19.79560.19431540.1727291697

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