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- PDB-5oh5: Legionella pneumophila RidL N-terminal retromer binding domain -

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Basic information

Entry
Database: PDB / ID: 5oh5
TitleLegionella pneumophila RidL N-terminal retromer binding domain
ComponentsRidL
KeywordsTOXIN / novel alpha helical fold
Function / homology:
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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: RidL


Theoretical massNumber of molelcules
Total (without water)32,0931
Polymers32,0931
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.140, 110.140, 98.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-382-

HOH

31A-470-

HOH

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Components

#1: Protein RidL


Mass: 32092.971 Da / Num. of mol.: 1
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.: 187 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49.255 Å / Num. obs: 24155 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.919 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.055 / Χ2: 0.958 / Net I/σ(I): 29.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.9513.3421.881.4817350.6551.95499.9
1.95-213.1281.2612.1517440.8751.31299.9
2-2.0612.8480.93.1216350.8870.938100
2.06-2.1212.260.644.3316280.9250.668100
2.12-2.1911.5270.475.6815840.9490.492100
2.19-2.2712.3440.3627.5915080.9710.377100
2.27-2.3612.6780.25410.4814880.9860.265100
2.36-2.4513.9220.19914.114260.9920.207100
2.45-2.5613.890.14618.6613630.9960.152100
2.56-2.6913.8070.11722.8913070.9970.122100
2.69-2.8313.6170.08829.4812390.9980.092100
2.83-313.4390.06338.9311860.9990.065100
3-3.2113.3940.04751.1611130.9990.049100
3.21-3.4712.940.03564.47104010.036100
3.47-3.811.8620.028779700.9990.03100
3.8-4.2511.1420.02485.0387410.026100
4.25-4.9112.4580.02393.9178610.02499.9
4.91-6.0113.9220.02497.467010.025100
6.01-8.513.3640.022101.5753510.023100
8.5-49.25511.7220.02106.813240.9990.02199.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.255 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.92
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 1206 4.99 %Random selection
Rwork0.204 ---
obs0.2045 24146 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.26 Å2 / Biso mean: 52.5412 Å2 / Biso min: 24.72 Å2
Refinement stepCycle: final / Resolution: 1.9→49.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 0 187 2333
Biso mean---50.93 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062183
X-RAY DIFFRACTIONf_angle_d0.842938
X-RAY DIFFRACTIONf_chiral_restr0.054318
X-RAY DIFFRACTIONf_plane_restr0.005391
X-RAY DIFFRACTIONf_dihedral_angle_d15.0481354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.97610.36451290.341924772606
1.9761-2.0660.27531330.287325192652
2.066-2.17490.29821320.264125152647
2.1749-2.31120.27241330.245425132646
2.3112-2.48960.25451330.234825282661
2.4896-2.74020.23371340.232625512685
2.7402-3.13660.27371340.223625452679
3.1366-3.95160.18371350.187225732708
3.9516-49.27150.17161430.16827192862
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)
11.4379-0.2680.38940.42640.23170.6458-0.11460.0352-0.19820.08990.1388-0.0963-0.25130.3297-0.00620.398-0.01230.04070.4010.02670.469333.764749.065719.6523
20.29390.1487-0.05010.13250.04110.5727-0.15-0.0066-0.17270.25130.34310.0295-0.20840.33380.01970.39290.0709-0.03570.41020.0160.708644.72743.122426.1818
31.73410.58830.16730.4071-0.30740.3021-0.04430.0424-0.3891-0.1630.0403-0.2115-0.034-0.0757-0.02090.33570.03050.03960.3282-0.04070.391121.111143.624613.006
4-0.18190.059-0.2110.68040.33630.74370.07680.1121-0.0806-0.1906-0.11190.083-0.1666-0.0369-0.0020.36870.02850.01030.35040.01250.248812.550571.394213.9369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 50 )A7 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 90 )A51 - 90
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 183 )A91 - 183
4X-RAY DIFFRACTION4chain 'A' and (resid 184 through 274 )A184 - 274

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