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- PDB-5wd8: Crystal structure of Legionella pneumophila effector lpg2328 -

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Basic information

Entry
Database: PDB / ID: 5wd8
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 / SAD / Resolution: 1.944 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lem22
B: Lem22


Theoretical massNumber of molelcules
Total (without water)21,3412
Polymers21,3412
Non-polymers00
Water3,135174
1
A: Lem22


Theoretical massNumber of molelcules
Total (without water)10,6711
Polymers10,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lem22


Theoretical massNumber of molelcules
Total (without water)10,6711
Polymers10,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.044, 81.143, 45.684
Angle α, β, γ (deg.)90.00, 90.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lem22 / lpg2328


Mass: 10670.622 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_2320 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G8UTY6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.988 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.94→40.575 Å / Num. obs: 12194 / % possible obs: 99.1 % / Redundancy: 6.6 % / Rsym value: 0.135 / Net I/σ(I): 19.9
Reflection shellResolution: 1.94→1.98 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1083 / Rsym value: 0.506 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.944→40.572 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.04
RfactorNum. reflection% reflection
Rfree0.2699 588 4.82 %
Rwork0.2161 --
obs0.2186 12194 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.944→40.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 0 174 1632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011474
X-RAY DIFFRACTIONf_angle_d0.3341974
X-RAY DIFFRACTIONf_dihedral_angle_d6.107926
X-RAY DIFFRACTIONf_chiral_restr0.026226
X-RAY DIFFRACTIONf_plane_restr0.002250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9444-1.980.32821500.24342766X-RAY DIFFRACTION95
2.14-2.44970.28241650.2262895X-RAY DIFFRACTION100
2.4497-3.08620.28221340.23682950X-RAY DIFFRACTION100
3.0862-4.18760.24341390.19592995X-RAY DIFFRACTION100
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)
10.31970.0599-0.07770.20110.20270.38570.0262-0.1015-0.051-0.01910.0266-0.12380.01970.193200.20670.0062-0.00420.1723-0.01840.1981-6.4065-1.3208-11.4545
20.0198-0.0860.01550.50140.03380.0866-0.34140.0581-0.2651-0.16160.04450.49820.24680.2694-0.00530.32170.07310.04350.35820.03170.2116-14.8493-3.83555.9286
30.5667-0.2143-0.02330.18330.21210.3759-0.12260.1876-0.09420.0924-0.25370.2660.065-0.3517-0.01040.18120.00030.00450.2295-0.00510.2223-14.9757-3.6784-17.1636
40.0191-0.05230.00910.15890.03290.14030.0847-0.153-0.2379-0.1396-0.03360.0940.2417-0.1524-0.0080.2343-0.008-0.02910.22280.01790.2052-4.8293-25.667-9.8704
50.111-0.0817-0.05910.07250.09360.1666-0.1452-0.1440.25380.0377-0.03820.10510.0292-0.2146-0.01440.22120.01060.01530.19360.00230.2595-2.583-17.6265-7.4826
60.525-0.1569-0.00730.2237-0.29070.4292-0.11280.0971-0.08420.0278-0.159-0.24840.05490.2453-0.0020.19480.0048-0.01310.2213-0.00630.22933.5486-19.2101-17.234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 96 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 33 )
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 63 )
6X-RAY DIFFRACTION6chain 'B' and (resid 64 through 97 )

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