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- PDB-7yji: Crystal structure of Lpg1083 from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 7yji
TitleCrystal structure of Lpg1083 from Legionella pneumophila
ComponentsT4SS effector Lpg1083
KeywordsAPOPTOSIS / T4SS Effector / Nuclear-Localization / Lamin-B2 / Importin-13
Function / homologyACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsGe, H. / Gao, J. / Chen, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970103 China
CitationJournal: J Mol Cell Biol / Year: 2023
Title: The bacterial effector SidN/Lpg1083 promotes cell death by targeting Lamin-B2.
Authors: Gao, J. / Xu, W. / Tang, F. / Xu, M. / Zhou, Q. / Yang, X. / Zhang, N. / Ma, J. / Yang, Q. / Chen, X. / Qin, X. / Ge, H.
History
DepositionJul 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T4SS effector Lpg1083
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6032
Polymers27,5431
Non-polymers591
Water1,856103
1
A: T4SS effector Lpg1083
hetero molecules

A: T4SS effector Lpg1083
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2054
Polymers55,0872
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area3360 Å2
ΔGint-31 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.660, 93.660, 136.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein T4SS effector Lpg1083


Mass: 27543.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_04810 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F9N6
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 287 K / Method: vapor diffusion
Details: 0.1 M sodium acetate, pH 4.6, 2.4 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97931 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.1→77.185 Å / Num. all: 17123 / Num. obs: 17123 / % possible obs: 94.7 % / Redundancy: 15.7 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.162 / Rsym value: 0.157 / Net I/av σ(I): 3.2 / Net I/σ(I): 12.3 / Num. measured all: 268633
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.2116.11.1260.74167125900.2891.1631.1262.9100
2.21-2.3516.10.6781.13216819990.1740.7010.6784.681.9
2.35-2.51160.4771.63725523260.1230.4920.4776.4100
2.51-2.71160.3142.43131719560.0810.3250.3148.990.7
2.71-2.9715.80.2043.53177320050.0530.210.20412.5100
2.97-3.3215.70.1314.92841718050.0340.1350.13117.5100
3.32-3.8315.60.1085.22156513860.0280.1120.1082286
3.83-4.715.10.11151966713050.0290.1150.11124.494.1
4.7-6.6414.20.10551555410930.0280.1090.10524100
6.64-77.18514.10.0786.692466580.0220.0810.07825.599.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→19.296 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 809 4.74 %
Rwork0.1821 16269 -
obs0.1845 17078 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.73 Å2 / Biso mean: 44.5839 Å2 / Biso min: 14.5 Å2
Refinement stepCycle: final / Resolution: 2.1→19.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1859 0 4 103 1966
Biso mean--72.75 43.88 -
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1001-2.23150.27331540.21862791100
2.2315-2.40350.2381050.1966241085
2.4035-2.64480.22571510.19072807100
2.6448-3.02620.24481210.191267293
3.0262-3.80790.26031250.1759266692
3.8079-19.2960.21151530.1716292397
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)
10.0857-0.20910.03080.7940.2640.43570.0024-0.124-0.05540.04490.0747-0.0172-0.4475-0.30230.18880.22890.185-0.00520.18490.08860.284-15.708418.03542.3069
20.12720.06080.08180.2902-0.00640.47650.0303-0.180.06560.2173-0.01540.0261-0.1924-0.0631-0.00010.21870.06690.04130.2487-0.00850.2161-12.367812.262413.9124
30.9455-0.32190.07811.05520.09381.0361-0.1317-0.35450.03490.06060.23770.1156-0.33020.03480.00010.34980.10530.02310.331-0.04510.2903-7.159120.387341.2998
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )A1 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 81 )A33 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 225 )A82 - 225

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