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- PDB-4fgd: Structure of the effector protein Tse1 from Pseudomonas aeruginos... -

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Basic information

Entry
Database: PDB / ID: 4fgd
TitleStructure of the effector protein Tse1 from Pseudomonas aeruginosa, selenomethionine variant
ComponentsTse1
KeywordsHYDROLASE / N1pC/P60 superfamily / peptidoglycan hydrolase / cytosol
Function / homology
Function and homology information


gamma-D-glutamyl-meso-diaminopimelate peptidase / amidase activity / host cell membrane / extracellular region / membrane
Similarity search - Function
endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Peptidoglycan amidase Tse1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsBenz, J. / Sendlmeier, C. / Barends, T.R.M. / Meinhart, A.
CitationJournal: Plos One / Year: 2012
Title: Structural Insights into the Effector - Immunity System Tse1/Tsi1 from Pseudomonas aeruginosa.
Authors: Benz, J. / Sendlmeier, C. / Barends, T.R. / Meinhart, A.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tse1
B: Tse1
C: Tse1
D: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9328
Polymers71,7234
Non-polymers2104
Water2,306128
1
A: Tse1


Theoretical massNumber of molelcules
Total (without water)17,9311
Polymers17,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tse1


Theoretical massNumber of molelcules
Total (without water)17,9311
Polymers17,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0473
Polymers17,9311
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0243
Polymers17,9311
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Tse1
C: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9774
Polymers35,8612
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-17 kcal/mol
Surface area13370 Å2
MethodPISA
6
B: Tse1
D: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9554
Polymers35,8612
Non-polymers942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-19 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.210, 108.400, 83.760
Angle α, β, γ (deg.)90.00, 93.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tse1


Mass: 17930.646 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1844 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9I2Q1
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM KSCN, 1% (v/v) MPD, and 15% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 21440 / Num. obs: 21546 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 8.4 / Num. unique all: 2189 / % possible all: 95.9

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Processing

Software
NameVersionClassification
SHELXDphasing
SHELXEmodel building
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→45.45 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.892 / SU B: 10.222 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.772 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25112 1072 5 %RANDOM
Rwork0.20559 ---
all0.2079 21546 --
obs0.2079 20367 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.638 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å2-0.22 Å2
2---1.27 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 10 128 4530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224490
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.946081
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3015584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67824.348184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43715714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2821524
X-RAY DIFFRACTIONr_chiral_restr0.0730.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023416
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21930
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.23076
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4181.52898
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81524579
X-RAY DIFFRACTIONr_scbond_it1.29831592
X-RAY DIFFRACTIONr_scangle_it2.0364.51502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 74 -
Rwork0.238 1408 -
obs--100 %

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