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- PDB-5wd9: Crystal structure of Legionella pneumophila effector lpg2328 -

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Basic information

Entry
Database: PDB / ID: 5wd9
TitleCrystal structure of Legionella pneumophila effector lpg2328
ComponentsLem22
KeywordsPROTEIN BINDING / bacterial effector / Legionella / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology:
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKozlov, G. / Wong, K. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Proteins / Year: 2018
Title: Crystal structure of the Legionella effector Lem22.
Authors: Kozlov, G. / Wong, K. / Gehring, K.
History
DepositionJul 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Structure summary / Category: citation / entity / entity_name_com
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lem22


Theoretical massNumber of molelcules
Total (without water)10,5301
Polymers10,5301
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.505, 24.852, 41.297
Angle α, β, γ (deg.)90.00, 114.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lem22 / lpg2328


Mass: 10529.937 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_2320 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G8UTY6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 1.85 Å3/Da / Density % sol: 33.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9779 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.4→22.44 Å / Num. obs: 15317 / % possible obs: 99 % / Redundancy: 5.8 % / Rsym value: 0.102 / Net I/σ(I): 19.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 8.8 / Num. unique obs: 1522 / Rsym value: 0.403 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000228600

Resolution: 1.4→22.44 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.46
RfactorNum. reflection% reflection
Rfree0.2029 761 4.97 %
Rwork0.1636 --
obs0.1656 15317 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→22.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms699 0 0 113 812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006739
X-RAY DIFFRACTIONf_angle_d0.759996
X-RAY DIFFRACTIONf_dihedral_angle_d1.657473
X-RAY DIFFRACTIONf_chiral_restr0.05114
X-RAY DIFFRACTIONf_plane_restr0.003126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4005-1.45050.1881590.15462888X-RAY DIFFRACTION99
1.4505-1.50860.18151470.14472931X-RAY DIFFRACTION100
1.5086-1.57720.2031420.16742914X-RAY DIFFRACTION100
1.5772-1.66040.2251600.15692936X-RAY DIFFRACTION100
1.6604-1.76430.19861530.17432887X-RAY DIFFRACTION95
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)
10.63910.20570.46190.62530.25330.6061-0.05160.13570.05180.01450.0629-0.0427-0.01980.26510.00260.0574-0.0117-0.00470.0706-0.00330.058412.41774.589912.0265
20.0655-0.1404-0.10290.28170.23060.19980.09510.4078-0.2753-0.0981-0.0845-0.01020.339-0.06150.15580.08480.02840.00440.1454-0.04150.094311.5337-4.69292.277
30.0180.070.02810.779-0.28960.38930.023-0.1580.14750.39910.01910.4142-0.1103-0.35470.02680.10520.00960.02090.087-0.00720.09552.02420.594415.4847
40.0455-0.02850.15120.0187-0.09710.52840.0083-0.2115-0.30820.2816-0.18470.67250.3555-0.2321-0.17710.2104-0.04010.0620.1618-0.02690.287-1.485812.196822.0275
50.13710.0255-0.19460.56230.52750.8502-0.0030.05830.063-0.0546-0.080.2142-0.0932-0.3178-0.00720.06550.0016-0.01410.0583-0.00620.06273.869911.634111.4071
60.1583-0.0831-0.18380.36860.03780.55580.16320.221-0.1056-0.1139-0.0501-0.0277-0.07840.22490.12270.08980.0097-0.00920.1007-0.02590.07285.42130.8772-2.1331
70.12340.03920.01810.325-0.22970.18360.09810.2284-0.1232-0.3971-0.1661-0.11940.16430.021-0.01510.22090.03520.01410.2604-0.08520.19717.4556-7.6325-10.7333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 65 )
5X-RAY DIFFRACTION5chain 'A' and (resid 66 through 78 )
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 89 )
7X-RAY DIFFRACTION7chain 'A' and (resid 90 through 94 )

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