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- PDB-3stq: Hypothetical protein PA2703 Pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 3stq
TitleHypothetical protein PA2703 Pseudomonas aeruginosa PAO1
ComponentsPutative uncharacterized protein
KeywordsTOXIN / coiled-coil / toxin-antitoxin system / Tsi2-Tse2 / T6SS / toxin immunity
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: 2.284 Å
AuthorsZou, T.T. / Wang, M.T. / Jin, Q. / Cui, S.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal structure of Pseudomonas aeruginosa Tsi2 reveals a stably folded superhelical antitoxin
Authors: Zou, T.T. / Yao, X. / Qin, B. / Zhang, M. / Cai, L.F. / Shang, W. / Svergun, D.I. / Wang, M.T. / Cui, S. / Jin, Q.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
E: Putative uncharacterized protein
F: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)67,8876
Polymers67,8876
Non-polymers00
Water3,027168
1
A: Putative uncharacterized protein
E: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)22,6292
Polymers22,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-18 kcal/mol
Surface area10400 Å2
MethodPISA
2
B: Putative uncharacterized protein
F: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)22,6292
Polymers22,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-22 kcal/mol
Surface area9390 Å2
MethodPISA
3
C: Putative uncharacterized protein

C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)22,6292
Polymers22,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556-x+1/2,y,-z+11
Buried area2820 Å2
ΔGint-19 kcal/mol
Surface area10760 Å2
MethodPISA
4
D: Putative uncharacterized protein

D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)22,6292
Polymers22,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_656-x+3/2,y,-z+11
Buried area2840 Å2
ΔGint-20 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.897, 113.265, 143.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein
Putative uncharacterized protein / Tsi2


Mass: 11314.463 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2703 / Plasmid: pET28a / 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.: 168 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 100mM Citric acid, 16%(v/v) MPD, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2010
RadiationMonochromator: Double Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.28→88.9 Å / Num. obs: 34226 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.73 % / Biso Wilson estimate: 44.168 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.69
Reflection shellResolution: 2.28→2.42 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 3.31 / Num. unique all: 10379 / % possible all: 97.4

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Processing

Software
NameVersionClassification
RemDAqdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.284→88.899 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8411 / SU ML: 0.29 / σ(F): 1.47 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 1710 5 %RANDOM
Rwork0.2081 ---
obs0.2095 34218 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.367 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 137.13 Å2 / Biso mean: 47.6666 Å2 / Biso min: 17.46 Å2
Baniso -1Baniso -2Baniso -3
1-3.3994 Å2-0 Å2-0 Å2
2---0.8293 Å2-0 Å2
3----2.5701 Å2
Refinement stepCycle: LAST / Resolution: 2.284→88.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 0 168 4094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083984
X-RAY DIFFRACTIONf_angle_d1.0965425
X-RAY DIFFRACTIONf_chiral_restr0.071612
X-RAY DIFFRACTIONf_plane_restr0.006747
X-RAY DIFFRACTIONf_dihedral_angle_d17.0611524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2836-2.35080.24321360.22352573270996
2.3508-2.42660.29331420.214827012843100
2.4266-2.51340.24471400.216126682808100
2.5134-2.6140.2711420.21827012843100
2.614-2.7330.26641410.219926702811100
2.733-2.87710.23941430.214827202863100
2.8771-3.05740.24271420.216726922834100
3.0574-3.29340.26771430.20727192862100
3.2934-3.62490.24571420.203627002842100
3.6249-4.14940.22211440.189727272871100
4.1494-5.22770.19961450.183227602905100
5.2277-88.96670.23051500.229228773027100

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