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- PDB-4f0v: Crystal structure of type effector Tse1 from Pseudomonas aeruginousa -

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Basic information

Entry
Database: PDB / ID: 4f0v
TitleCrystal structure of type effector Tse1 from Pseudomonas aeruginousa
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / NlpC/P60 domain / type VI amidase effector
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
SUCCINIC ACID / Peptidoglycan amidase Tse1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Febs Lett. / Year: 2012
Title: Crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa.
Authors: Zhang, H. / Gao, Z.Q. / Su, X.D. / Dong, Y.H.
History
DepositionMay 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3152
Polymers20,1971
Non-polymers1181
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.265, 61.723, 74.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein / type effector Tse1


Mass: 20196.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1844 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I2Q1
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Succinic acid pH 7.0, 15% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 5, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 23887 / Num. obs: 23887 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 67.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 11.3 / Num. unique all: 1164 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.autosol: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→32.522 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 15.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1721 1220 5.12 %RANDOM
Rwork0.1558 ---
all0.1566 23887 --
obs0.1566 23809 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.238 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1767 Å20 Å20 Å2
2---3.7214 Å2-0 Å2
3----2.4552 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1134 0 8 196 1338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061169
X-RAY DIFFRACTIONf_angle_d0.9571583
X-RAY DIFFRACTIONf_dihedral_angle_d12.622420
X-RAY DIFFRACTIONf_chiral_restr0.063170
X-RAY DIFFRACTIONf_plane_restr0.003207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6001-1.66420.23791180.18132488
1.6642-1.73990.17361250.16342465
1.7399-1.83160.17791670.15162422
1.8316-1.94640.18031220.14992497
1.9464-2.09660.16061460.1482481
2.0966-2.30750.1821490.15082483
2.3075-2.64130.17591230.15782520
2.6413-3.32730.19981390.15722562
3.3273-32.5290.14521310.15582671
Refinement TLS params.Method: refined / Origin x: -0.1357 Å / Origin y: -18.4117 Å / Origin z: 13.5131 Å
111213212223313233
T0.0729 Å2-0.0077 Å2-0.0019 Å2-0.0774 Å20.0002 Å2--0.0777 Å2
L0.4333 °20.0608 °2-0.034 °2-0.4698 °20.1964 °2--0.6018 °2
S0.0173 Å °-0.0386 Å °0.0117 Å °0.0136 Å °-0.0002 Å °0.0274 Å °-0.006 Å °0.0225 Å °0.0059 Å °
Refinement TLS groupSelection details: ALL

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