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- PDB-4fge: Structure of the effector protein Tse1 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4fge
TitleStructure of the effector protein Tse1 from Pseudomonas aeruginosa
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 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
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)71,37911
Polymers70,9724
Non-polymers4077
Water5,945330
1
A: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8724
Polymers17,7431
Non-polymers1293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8933
Polymers17,7431
Non-polymers1502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7792
Polymers17,7431
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8352
Polymers17,7431
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Tse1
C: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6516
Polymers35,4862
Non-polymers1644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
B: Tse1
D: Tse1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7285
Polymers35,4862
Non-polymers2423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.240, 100.380, 62.180
Angle α, β, γ (deg.)90.00, 99.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tse1


Mass: 17743.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1844 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9I2Q1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM KSCN, 1% (v/v) MPD, and 20% (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: 0.9796 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 64182 / Num. obs: 63172 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3.13 / Num. unique all: 9887 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.075 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20269 3158 5 %RANDOM
Rwork0.17512 ---
all0.17648 64182 --
obs0.17648 60001 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: 31.008 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.67 Å2
2--0.41 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4437 0 21 330 4788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224638
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.9446302
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1145624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5424.136191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42715749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4261528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023552
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.22122
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23215
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4521.52982
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82624739
X-RAY DIFFRACTIONr_scbond_it1.37231656
X-RAY DIFFRACTIONr_scangle_it2.2184.51547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 230 -
Rwork0.253 4387 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1316-0.3984-0.75232.3085-0.24683.40120.03410.2960.4535-0.1030.04540.0491-0.3402-0.1023-0.0795-0.18510.0111-0.0032-0.14810.0266-0.100628.56578.05557.7846
23.98530.5941-0.55485.0192-1.02734.37090.1186-0.0285-0.1268-0.0559-0.05490.09680.06750.0661-0.0637-0.1089-0.02530.0201-0.19360.0157-0.1306-6.2487-28.449716.9321
33.7856-0.025-0.28382.71840.00373.0802-0.1584-0.2348-0.12810.27330.0261-0.05920.1805-0.00470.1324-0.1896-0.001-0.0049-0.1566-0.0123-0.1816.5071-4.379626.0948
44.0174-0.4136-0.75134.86240.19964.6440.07430.2928-0.1319-0.43-0.02090.02790.17780.031-0.0534-0.06570.00980.0078-0.08870.0179-0.196-7.2518-9.1727-11.6372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 149
2X-RAY DIFFRACTION2B4 - 149
3X-RAY DIFFRACTION3C3 - 150
4X-RAY DIFFRACTION4D4 - 150

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