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- PDB-3vpj: crystal structure of type VI effector Tse1 from Pseudomonas aerug... -

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Basic information

Entry
Database: PDB / ID: 3vpj
Titlecrystal structure of type VI effector Tse1 from Pseudomonas aeruginosa in complex with immune protein Tsi1
Components
  • Tse1-specific immunity protein
  • type VI secretion exported 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


gamma-D-glutamyl-meso-diaminopimelate peptidase / amidase activity / host cell membrane / extracellular region / membrane
Similarity search - Function
Lipocalin - #650 / : / : / Immune protein Tsi1 / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Lipocalin / Alpha-Beta Complex / Beta Barrel ...Lipocalin - #650 / : / : / Immune protein Tsi1 / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Lipocalin / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immune protein Tsi1 / Peptidoglycan amidase Tse1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDing, J. / Wang, W. / Wang, D.C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural insights into the Pseudomonas aeruginosa type VI virulence effector Tse1 bacteriolysis and self-protection mechanisms
Authors: Ding, J. / Wang, W. / Feng, H. / Zhang, Y. / Wang, D.C.
History
DepositionMar 4, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 secretion exported 1
B: type VI secretion exported 1
E: Tse1-specific immunity protein
F: Tse1-specific immunity protein
C: type VI secretion exported 1
D: type VI secretion exported 1
G: Tse1-specific immunity protein
H: Tse1-specific immunity protein


Theoretical massNumber of molelcules
Total (without water)158,3188
Polymers158,3188
Non-polymers00
Water6,143341
1
A: type VI secretion exported 1
E: Tse1-specific immunity protein


Theoretical massNumber of molelcules
Total (without water)39,5792
Polymers39,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-4 kcal/mol
Surface area13190 Å2
MethodPISA
2
B: type VI secretion exported 1
F: Tse1-specific immunity protein


Theoretical massNumber of molelcules
Total (without water)39,5792
Polymers39,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-2 kcal/mol
Surface area13120 Å2
MethodPISA
3
C: type VI secretion exported 1
G: Tse1-specific immunity protein


Theoretical massNumber of molelcules
Total (without water)39,5792
Polymers39,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-2 kcal/mol
Surface area13310 Å2
MethodPISA
4
D: type VI secretion exported 1
H: Tse1-specific immunity protein


Theoretical massNumber of molelcules
Total (without water)39,5792
Polymers39,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-3 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.000, 97.000, 292.171
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
type VI secretion exported 1


Mass: 18630.045 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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2Q1
#2: Protein
Tse1-specific immunity protein


Mass: 20949.334 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1845 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2Q0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 20% PEG 4000, 20% isopropanol, 0.1M sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→63.61 Å / Num. all: 56237 / Num. obs: 56166 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 56.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 21.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 5.6 / Num. unique all: 8041 / Rsym value: 0.387 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.97 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8012 / SU ML: 0.37 / σ(F): 0 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 2818 5.08 %RANDOM
Rwork0.2069 ---
obs0.2095 55504 98.7 %-
all-56166 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.518 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 113.58 Å2 / Biso mean: 52.87 Å2 / Biso min: 18.74 Å2
Baniso -1Baniso -2Baniso -3
1-2.8463 Å20 Å2-0 Å2
2--2.8463 Å20 Å2
3----5.6927 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8904 0 0 341 9245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119388
X-RAY DIFFRACTIONf_angle_d1.05912295
X-RAY DIFFRACTIONf_dihedral_angle_d14.3693308
X-RAY DIFFRACTIONf_chiral_restr0.0761292
X-RAY DIFFRACTIONf_plane_restr0.0041646
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.54310.31981310.2736254495
2.5431-2.58940.32921310.2826248696
2.5894-2.63920.40391330.2828253297
2.6392-2.6930.32311450.2819256497
2.693-2.75160.40291370.2813254798
2.7516-2.81560.32571250.2637260599
2.8156-2.8860.34081260.2583259798
2.886-2.9640.28811490.2579258299
2.964-3.05120.36741580.2483262599
3.0512-3.14970.26831410.2507262899
3.1497-3.26220.29891430.242611100
3.2622-3.39280.28451480.2434263299
3.3928-3.54720.29281380.22082657100
3.5472-3.73410.27471440.2112693100
3.7341-3.9680.24721520.19322634100
3.968-4.27420.22591460.17122691100
4.2742-4.70390.18111420.1472685100
4.7039-5.38380.1971430.1522742100
5.3838-6.780.2441400.19782746100
6.78-47.97870.18551460.1764288599

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