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- PDB-4f4m: Structure of the type VI peptidoglycan amidase effector Tse1 (C30... -

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Basic information

Entry
Database: PDB / ID: 4f4m
TitleStructure of the type VI peptidoglycan amidase effector Tse1 (C30A) from Pseudomonas aeruginosa
Componentspapain peptidoglycan amidase effector Tse1
KeywordsHydrolase regulator / papain peptidoglycan amidase effector / amidase / Tsi1
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 / MOLECULAR REPLACEMENT / Resolution: 2.677 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
DepositionMay 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: papain peptidoglycan amidase effector Tse1
B: papain peptidoglycan amidase effector Tse1
C: papain peptidoglycan amidase effector Tse1
D: papain peptidoglycan amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)69,0224
Polymers69,0224
Non-polymers00
Water00
1
A: papain peptidoglycan amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,2551
Polymers17,2551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: papain peptidoglycan amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,2551
Polymers17,2551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: papain peptidoglycan amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,2551
Polymers17,2551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: papain peptidoglycan amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,2551
Polymers17,2551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.018, 108.857, 82.531
Angle α, β, γ (deg.)90.00, 93.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
papain peptidoglycan amidase effector Tse1


Mass: 17255.490 Da / Num. of mol.: 4 / Fragment: Tse1 C30A / Mutation: C30A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1844 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I2Q1

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were obtained by sitting drop vapor diffusion at 25 oC from a 1:1 mixture of 10 mg/mL protein with 0.2 M sodium thiocyanate, 0.1 M HEPES (pH 7.5), 20% PEG3350 for 3 days. Crystals ...Details: Crystals were obtained by sitting drop vapor diffusion at 25 oC from a 1:1 mixture of 10 mg/mL protein with 0.2 M sodium thiocyanate, 0.1 M HEPES (pH 7.5), 20% PEG3350 for 3 days. Crystals were immersed in mother liquor containing 20% glycerol, mounted, and flash frozen in liquid N2. , VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2012
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.677→65.69 Å / Num. all: 19092 / Num. obs: 19072 / % possible obs: 100 % / Biso Wilson estimate: 18.61 Å2 / Rmerge(I) obs: 0.136

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXPhasermodel building
PHENIX(phenix.refine: dev_1047)refinement
XDSdata reduction
PHENIXPhaserphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.677→65.69 Å / SU ML: 0.31 / σ(F): 1.36 / Phase error: 24.54 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.243 981 5.15 %Random
Rwork0.2035 ---
all0.234 19092 --
obs0.2056 19064 95.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.677→65.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 0 0 4360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084452
X-RAY DIFFRACTIONf_angle_d1.1126032
X-RAY DIFFRACTIONf_dihedral_angle_d14.1211568
X-RAY DIFFRACTIONf_chiral_restr0.078652
X-RAY DIFFRACTIONf_plane_restr0.003784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6767-2.81790.28021210.23992387X-RAY DIFFRACTION89
2.8179-2.99440.30521400.23662626X-RAY DIFFRACTION97
2.9944-3.22560.30621530.242618X-RAY DIFFRACTION97
3.2256-3.55020.27431530.21492608X-RAY DIFFRACTION98
3.5502-4.06380.19991330.19352646X-RAY DIFFRACTION97
4.0638-5.11970.19951420.16672627X-RAY DIFFRACTION97
5.1197-65.71020.20661390.18042571X-RAY DIFFRACTION94

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