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- PDB-4eob: Structure of the type VI peptidoglycan amidase effector Tse1 from... -

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Basic information

Entry
Database: PDB / ID: 4eob
TitleStructure of the type VI peptidoglycan amidase effector Tse1 from Pseudomonas aeruginosa
Componentstype VI amidase effector Tse1
KeywordsHYDROLASE / amidase / protease / bacteriolytic / peptidoglycan degrading / Tsi1 / PA1845
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
Peptidoglycan amidase Tse1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.611 Å
AuthorsChou, S. / Mougous, J.D.
CitationJournal: Cell Rep / Year: 2012
Title: Structure of a peptidoglycan amidase effector targeted to Gram-negative bacteria by the type VI secretion system.
Authors: Chou, S. / Bui, N.K. / Russell, A.B. / Lexa, K.W. / Gardiner, T.E. / LeRoux, M. / Vollmer, W. / Mougous, J.D.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references / Structure summary
Revision 1.2Jul 11, 2012Group: Database references
Revision 1.3Mar 27, 2013Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / 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: type VI amidase effector Tse1
B: type VI amidase effector Tse1
C: type VI amidase effector Tse1
D: type VI amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)70,1194
Polymers70,1194
Non-polymers00
Water2,900161
1
A: type VI amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,5301
Polymers17,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: type VI amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,5301
Polymers17,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: type VI amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,5301
Polymers17,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: type VI amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,5301
Polymers17,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: type VI amidase effector Tse1
B: type VI amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)35,0602
Polymers35,0602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8 kcal/mol
Surface area13030 Å2
MethodPISA
6
C: type VI amidase effector Tse1
D: type VI amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)35,0602
Polymers35,0602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.662, 107.578, 84.396
Angle α, β, γ (deg.)90.00, 94.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
type VI amidase effector Tse1


Mass: 17529.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1844 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle BL21 / References: UniProt: Q9I2Q1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 100mM Sodium thiocyanate, 18% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: KHOZU double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.61→45.32 Å / Num. obs: 20654 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 27.11 Å2 / Rmerge(I) obs: 0.234 / Rsym value: 0.234 / Net I/σ(I): 7.81
Reflection shellResolution: 2.61→2.66 Å / % possible all: 94.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXPhasermodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXPhaserphasing
RefinementMethod to determine structure: SAD / Resolution: 2.611→45.32 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 3732 9.71 %
Rwork0.1864 --
obs-20654 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.7475 Å2-0 Å28.0428 Å2
2---10.2911 Å2-0 Å2
3---6.4174 Å2
Refinement stepCycle: LAST / Resolution: 2.611→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 0 161 4522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084453
X-RAY DIFFRACTIONf_angle_d1.136033
X-RAY DIFFRACTIONf_dihedral_angle_d14.1631569
X-RAY DIFFRACTIONf_chiral_restr0.078652
X-RAY DIFFRACTIONf_plane_restr0.004784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6108-2.64380.36171070.24321048X-RAY DIFFRACTION76
2.6438-2.67860.32521390.24041114X-RAY DIFFRACTION85
2.6786-2.71530.33461210.2371251X-RAY DIFFRACTION86
2.7153-2.75410.31631320.24031216X-RAY DIFFRACTION88
2.7541-2.79520.31221500.21891180X-RAY DIFFRACTION90
2.7952-2.83880.32211120.21771219X-RAY DIFFRACTION88
2.8388-2.88540.30241410.2051265X-RAY DIFFRACTION92
2.8854-2.93510.24361260.21211272X-RAY DIFFRACTION90
2.9351-2.98850.28251440.22571298X-RAY DIFFRACTION92
2.9885-3.04590.30941150.22361224X-RAY DIFFRACTION93
3.0459-3.10810.25551400.21951275X-RAY DIFFRACTION93
3.1081-3.17570.30281500.21341324X-RAY DIFFRACTION94
3.1757-3.24950.25611370.20031313X-RAY DIFFRACTION94
3.2495-3.33080.20321290.19611279X-RAY DIFFRACTION96
3.3308-3.42080.23011520.1861348X-RAY DIFFRACTION96
3.4208-3.52140.2411450.18871338X-RAY DIFFRACTION96
3.5214-3.6350.26851260.17931273X-RAY DIFFRACTION96
3.635-3.76490.19421760.15881353X-RAY DIFFRACTION97
3.7649-3.91550.22871360.15971372X-RAY DIFFRACTION97
3.9155-4.09360.25261250.16461354X-RAY DIFFRACTION98
4.0936-4.30930.18241510.15181362X-RAY DIFFRACTION98
4.3093-4.5790.18341470.14561327X-RAY DIFFRACTION98
4.579-4.93220.21491510.15561359X-RAY DIFFRACTION98
4.9322-5.42780.19411460.18041328X-RAY DIFFRACTION97
5.4278-6.21150.25681470.22011312X-RAY DIFFRACTION97
6.2115-7.81930.24621450.17391357X-RAY DIFFRACTION97
7.8193-45.33070.22891420.18631345X-RAY DIFFRACTION98

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