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- PDB-5ot4: Structure of the Legionella pneumophila effector RidL (1-866) -

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Basic information

Entry
Database: PDB / ID: 5ot4
TitleStructure of the Legionella pneumophila effector RidL (1-866)
ComponentsInteraptin
KeywordsTRANSPORT PROTEIN / Retromer / Legionella pneumophila
Function / homology: / Interaptin
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsRomano-Moreno, M. / Rojas, A.L. / Lucas, M. / Isupov, M.N. / Hierro, A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular mechanism for the subversion of the retromer coat by the Legionella effector RidL.
Authors: Romano-Moreno, M. / Rojas, A.L. / Williamson, C.D. / Gershlick, D.C. / Lucas, M. / Isupov, M.N. / Bonifacino, J.S. / Machner, M.P. / Hierro, A.
History
DepositionAug 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 9, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Interaptin
B: Interaptin
C: Interaptin
D: Interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,1195
Polymers406,0274
Non-polymers921
Water00
1
A: Interaptin


Theoretical massNumber of molelcules
Total (without water)101,5071
Polymers101,5071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5992
Polymers101,5071
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Interaptin


Theoretical massNumber of molelcules
Total (without water)101,5071
Polymers101,5071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Interaptin


Theoretical massNumber of molelcules
Total (without water)101,5071
Polymers101,5071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)242.648, 230.909, 86.726
Angle α, β, γ (deg.)90.000, 90.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Interaptin


Mass: 101506.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lp12_2303 / Production host: Escherichia coli (E. coli) / References: UniProt: G8UZ99, UniProt: Q5ZT54*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.4 M sodium fluoride, 14-16% PEG 3350 0.1 M Bis-tris propane pH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3→167.27 Å / Num. obs: 93761 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.954 % / Biso Wilson estimate: 104.762 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.101 / Χ2: 1.012 / Net I/σ(I): 12.6 / Num. measured all: 651993
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.196.5462.3150.749719915184148490.3412.51797.8
3.19-3.417.2371.0791.7210277914321142020.7661.16299.2
3.41-3.687.0910.5173.69381213337132300.9290.55899.2
3.68-4.036.7480.2377.328230712298121980.9820.25799.2
4.03-4.57.2230.1214.067994711141110680.9950.12999.3
4.5-5.196.8240.07520.3266456980497390.9980.08199.3
5.19-6.337.2610.06324.660539835483380.9980.06799.8
6.33-8.886.8190.03537.8544094650164660.9990.03899.5
8.88-167.276.7720.0356.1124860372936710.9990.03298.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3→167.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 32.879 / SU ML: 0.536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.487 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2949 4953 5.2 %RANDOM
Rwork0.2286 ---
obs0.2321 89952 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 220 Å2 / Biso mean: 122.624 Å2 / Biso min: 58.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å23.95 Å2
2--5.09 Å20 Å2
3----3.95 Å2
Refinement stepCycle: final / Resolution: 3→167.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26226 0 6 0 26232
Biso mean--166.75 --
Num. residues----3311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01926634
X-RAY DIFFRACTIONr_bond_other_d0.0020.0225185
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.97735888
X-RAY DIFFRACTIONr_angle_other_deg1.07358788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.59753297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.74125.6011282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.121155091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.42215143
X-RAY DIFFRACTIONr_chiral_restr0.0860.24034
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0229382
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024897
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 349 -
Rwork0.434 6630 -
all-6979 -
obs--99.71 %

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