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- PDB-5xmg: Crystal structure of PA3488 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5xmg
TitleCrystal structure of PA3488 from Pseudomonas aeruginosa
ComponentsUncharacterized protein
KeywordsIMMUNE SYSTEM / immunity protein
Function / homologyTle cognate immunity protein 4, C-terminal domain / Tle cognate immunity protein 4 C-terminal domain / : / Tle cognate immunity protein 4 C-terminal domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsShe, Z. / Gao, Z.Q.
CitationJournal: Protein Sci. / Year: 2017
Title: Structural and SAXS analysis of Tle5-Tli5 complex reveals a novel inhibition mechanism of H2-T6SS in Pseudomonas aeruginosa.
Authors: Yang, X.Y. / Li, Z.Q. / Gao, Z.Q. / Wang, W.J. / Geng, Z. / Xu, J.H. / She, Z. / Dong, Y.H.
History
DepositionMay 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)43,3701
Polymers43,3701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17110 Å2
Unit cell
Length a, b, c (Å)66.390, 66.390, 363.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Uncharacterized protein / immunity protein


Mass: 43370.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: BZY57_06770, BZY58_00015 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1T2VI60, UniProt: A0A232D7B1*PLUS
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: 2.81 Å3/Da / Density % sol: 56.26 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Ammonium sulfate , 0.05 M BIS-TRIS pH 6.5, 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 22110 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.2
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 3.71 / Num. unique obs: 1661 / CC1/2: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→41.722 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 26.74
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2671 1122 5.08 %
Rwork0.2149 --
obs0.2175 22108 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→41.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 0 0 2793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122865
X-RAY DIFFRACTIONf_angle_d1.4223878
X-RAY DIFFRACTIONf_dihedral_angle_d17.2241721
X-RAY DIFFRACTIONf_chiral_restr0.066406
X-RAY DIFFRACTIONf_plane_restr0.009505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.92750.43071390.36342633X-RAY DIFFRACTION100
2.9275-3.08180.31131460.29872614X-RAY DIFFRACTION100
3.0818-3.27480.34181410.26462619X-RAY DIFFRACTION100
3.2748-3.52750.32231370.25652631X-RAY DIFFRACTION100
3.5275-3.88230.26021390.22512631X-RAY DIFFRACTION100
3.8823-4.44350.23411430.1842625X-RAY DIFFRACTION100
4.4435-5.59620.21941360.18212605X-RAY DIFFRACTION100
5.5962-41.72690.26041410.18752628X-RAY DIFFRACTION100

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