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- PDB-5oh6: Legionella pneumophila RidL N-terminal domain lacking beta hairpin -

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Basic information

Entry
Database: PDB / ID: 5oh6
TitleLegionella pneumophila RidL N-terminal domain lacking beta hairpin
ComponentsInteraptin
KeywordsTOXIN / novel alpha helical fold
Function / homology:
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsBaerlocher, K. / Hutter, C.A.J. / Swart, A.L. / Steiner, B. / Welin, A. / Hohl, M. / Letourneur, F. / Seeger, M.A. / Hilbi, H.
CitationJournal: Nat Commun / Year: 2017
Title: Structural insights into Legionella RidL-Vps29 retromer subunit interaction reveal displacement of the regulator TBC1D5.
Authors: Barlocher, K. / Hutter, C.A.J. / Swart, A.L. / Steiner, B. / Welin, A. / Hohl, M. / Letourneur, F. / Seeger, M.A. / Hilbi, H.
History
DepositionJul 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.name
Revision 1.2May 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

Downloads & links

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Assembly

Deposited unit
A: Interaptin
B: Interaptin


Theoretical massNumber of molelcules
Total (without water)53,1892
Polymers53,1892
Non-polymers00
Water2,252125
1
A: Interaptin


Theoretical massNumber of molelcules
Total (without water)26,5951
Polymers26,5951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interaptin


Theoretical massNumber of molelcules
Total (without water)26,5951
Polymers26,5951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.100, 58.050, 94.420
Angle α, β, γ (deg.)90.000, 98.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interaptin


Mass: 26594.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
Gene: lp12_2303 / Plasmid: pBXNH3 / Production host: Escherichia coli (E. coli) / Variant (production host): MC1061 / References: UniProt: G8UZ99
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→49.309 Å / Num. obs: 26742 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.868 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 1.053 / Net I/σ(I): 15.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.16.8570.7852.3219890.8880.84898.6
2.1-2.166.8830.7122.6118850.8750.76998.3
2.16-2.226.8990.5223.419140.9390.56499.4
2.22-2.296.860.4074.2117960.9640.4498.8
2.29-2.376.7320.3564.8617810.9690.38698.7
2.37-2.456.5870.2816.0616760.9810.30598.6
2.45-2.546.4320.2327.2715730.9830.25294.3
2.54-2.657.2880.1919.3915870.990.20699.7
2.65-2.767.2140.15711.2115240.9940.16999.2
2.76-2.97.1560.11614.2914850.9950.12599.7
2.9-3.067.0730.0971714070.9960.10499.6
3.06-3.246.9580.07121.2612930.9970.07799.1
3.24-3.476.7440.05825.6812360.9980.06399
3.47-3.746.4230.04531.4110920.9980.04993
3.74-4.17.0760.04138.110740.9990.04499.8
4.1-4.586.9540.03841.339660.9990.04299.7
4.58-5.296.8530.03542.58590.9990.03899.7
5.29-6.486.5770.03541.027360.9990.03899.2
6.48-9.176.7510.03251.455350.9990.03493.7
9.17-49.3096.7220.02559.43340.9990.02899.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
Cootmodel building
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OH6

Resolution: 2.05→49.309 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.66
RfactorNum. reflection% reflection
Rfree0.2422 1331 4.99 %
Rwork0.2017 --
obs0.2037 26681 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.92 Å2 / Biso mean: 59.1757 Å2 / Biso min: 26.68 Å2
Refinement stepCycle: final / Resolution: 2.05→49.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 0 125 3821
Biso mean---52.67 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033753
X-RAY DIFFRACTIONf_angle_d0.5725044
X-RAY DIFFRACTIONf_chiral_restr0.036548
X-RAY DIFFRACTIONf_plane_restr0.005676
X-RAY DIFFRACTIONf_dihedral_angle_d15.2872326
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.12330.3431330.32122534266798
2.1233-2.20830.31711330.28232522265599
2.2083-2.30880.32681320.26172502263498
2.3088-2.43060.281340.25422532266699
2.4306-2.58280.28441270.2422451257896
2.5828-2.78220.29591350.24782566270199
2.7822-3.06220.29731350.238825712706100
3.0622-3.50520.24381320.21632544267699
3.5052-4.41570.21781340.16862529266397
4.4157-49.32280.19271360.1612599273598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0299-0.0918-1.03831.7887-0.15622.27810.0992-0.18330.1507-0.1005-0.19080.2051-0.01920.3081-00.46970.00240.00720.4192-0.00950.428119.179859.7493-3.0091
21.75880.3532-0.8982.03051.05482.1663-0.1317-0.1615-0.1443-0.10880.00360.0856-0.04110.1234-0.00070.3024-0.0277-0.00450.40330.0340.39064.584259.522819.4554
32.2153-0.5956-2.37530.93860.91052.509-0.1998-0.02750.2790.04890.24430.13980.26280.1385-00.5070.06540.03340.46960.06750.519.158370.321159.5647
41.09660.0327-0.99360.48140.22412.9543-0.09430.0712-0.04780.06010.0648-0.07270.18780.181-0.00020.3201-0.0049-0.03030.3187-0.03520.34923.999965.496136.2861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 122 )A8 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 242 )A123 - 242
3X-RAY DIFFRACTION3chain 'B' and (resid 8 through 122 )B8 - 122
4X-RAY DIFFRACTION4chain 'B' and (resid 123 through 243 )B123 - 243

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