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- PDB-6lch: Pseudomonas aeruginosa 5086 (PA5086) -

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Basic information

Entry
Database: PDB / ID: 6lch
TitlePseudomonas aeruginosa 5086 (PA5086)
ComponentsSel1 repeat family protein
KeywordsPROTEIN BINDING / T6SS / Immunity protein
Function / homology: / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Tetratricopeptide-like helical domain superfamily / Sel1 repeat family protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsShe, Z. / Geng, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504900 China
National Natural Science Foundation of China (NSFC)31700651 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Characterization of the Pseudomonas aeruginosa T6SS PldB immunity proteins PA5086, PA5087 and PA5088 explains a novel stockpiling mechanism.
Authors: Wen, H. / Geng, Z. / Gao, Z. / She, Z. / Dong, Y.
History
DepositionNov 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sel1 repeat family protein


Theoretical massNumber of molelcules
Total (without water)30,6431
Polymers30,6431
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.100, 63.200, 66.900
Angle α, β, γ (deg.)90.000, 105.000, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-540-

HOH

31A-542-

HOH

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Components

#1: Protein Sel1 repeat family protein


Mass: 30642.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: DT376_05275 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A367MEJ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium sulfate decahydrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.899→50 Å / Num. obs: 18536 / % possible obs: 96.6 % / Redundancy: 7.5 % / CC1/2: 0.999 / Net I/σ(I): 25
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 1291 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JKP

5jkp


Resolution: 1.899→32.888 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 25.33
RfactorNum. reflection% reflection
Rfree0.2662 952 5.14 %
Rwork0.2291 --
obs0.231 18536 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 46.7 Å2 / Biso mean: 13.8274 Å2 / Biso min: 0.42 Å2
Refinement stepCycle: final / Resolution: 1.899→32.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 0 256 2341
Biso mean---19.93 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052154
X-RAY DIFFRACTIONf_angle_d0.7452935
X-RAY DIFFRACTIONf_chiral_restr0.045299
X-RAY DIFFRACTIONf_plane_restr0.005383
X-RAY DIFFRACTIONf_dihedral_angle_d5.9331282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.899-1.99880.33181230.2789244295
1.9988-2.1240.29661460.2354248397
2.124-2.2880.26781320.2279242293
2.288-2.51810.25441270.2308246495
2.5181-2.88230.25081460.2243255198
2.8823-3.63070.27021360.2161257599
3.6307-32.8880.24271420.22332647100

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