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- PDB-7c0q: a Legionella pneumophila effector Lpg2505 -

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Basic information

Entry
Database: PDB / ID: 7c0q
Titlea Legionella pneumophila effector Lpg2505
Componentseffector Lpg2505
KeywordsTOXIN / effector
Function / homologyProtein of unknown function DUF5630 / Family of unknown function (DUF5630) / Ankyrin repeat protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsChen, T.T. / Han, A.D. / Luo, Z.Q. / McCloskey, A. / Perri, K.
Funding support United States, China, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01AI127465 United States
National Natural Science Foundation of China (NSFC)31770803 China
National Natural Science Foundation of China (NSFC)81861138047 China
CitationJournal: Microbes Infect. / Year: 2021
Title: The metaeffector MesI regulates the activity of the Legionella effector SidI through direct protein-protein interactions.
Authors: McCloskey, A. / Perri, K. / Chen, T. / Han, A. / Luo, Z.Q.
History
DepositionMay 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: effector Lpg2505
B: effector Lpg2505
C: effector Lpg2505
D: effector Lpg2505
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4708
Polymers145,1014
Non-polymers3684
Water3,585199
1
A: effector Lpg2505
C: effector Lpg2505
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7354
Polymers72,5512
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-30 kcal/mol
Surface area25840 Å2
MethodPISA
2
B: effector Lpg2505
D: effector Lpg2505
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7354
Polymers72,5512
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-31 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.542, 50.448, 122.029
Angle α, β, γ (deg.)90.000, 109.060, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))
21(chain B and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))
31(chain C and (resid -3 through 74 or resid 76 through 274 or resid 301))
41(chain D and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISSERSER(chain A and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))AA-3 - 5620 - 79
12GLUGLULYSLYS(chain A and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))AA58 - 7481 - 97
13HISHISPHEPHE(chain A and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))AA76 - 27499 - 297
14GOLGOLGOLGOL(chain A and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))AE301
21HISHISSERSER(chain B and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))BB-3 - 5620 - 79
22GLUGLULYSLYS(chain B and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))BB58 - 7481 - 97
23HISHISPHEPHE(chain B and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))BB76 - 27499 - 297
24GOLGOLGOLGOL(chain B and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))BF301
31HISHISLYSLYS(chain C and (resid -3 through 74 or resid 76 through 274 or resid 301))CC-3 - 7420 - 97
32HISHISPHEPHE(chain C and (resid -3 through 74 or resid 76 through 274 or resid 301))CC76 - 27499 - 297
33GOLGOLGOLGOL(chain C and (resid -3 through 74 or resid 76 through 274 or resid 301))CG301
41HISHISSERSER(chain D and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))DD-3 - 5620 - 79
42GLUGLULYSLYS(chain D and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))DD58 - 7481 - 97
43HISHISPHEPHE(chain D and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))DD76 - 27499 - 297
44GOLGOLGOLGOL(chain D and (resid -3 through 56 or resid 58 through 74 or resid 76 through 274 or resid 301))DH301

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Components

#1: Protein
effector Lpg2505


Mass: 36275.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg2505 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSL2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 233 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→92.236 Å / Num. obs: 35768 / % possible obs: 98.2 % / Redundancy: 6.9 % / CC1/2: 0.995 / Net I/σ(I): 14.227
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.2 % / Num. unique obs: 37795 / CC1/2: 0.721 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→92.236 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 1822 5.09 %
Rwork0.2285 33945 -
obs0.2309 35767 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.65 Å2 / Biso mean: 38.5923 Å2 / Biso min: 6.92 Å2
Refinement stepCycle: final / Resolution: 2.6→92.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8857 0 56 199 9112
Biso mean--39.18 27.45 -
Num. residues----1099
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3316X-RAY DIFFRACTION16.009TORSIONAL
12B3316X-RAY DIFFRACTION16.009TORSIONAL
13C3316X-RAY DIFFRACTION16.009TORSIONAL
14D3316X-RAY DIFFRACTION16.009TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.67030.33921050.2742197392
2.6703-2.74890.32931290.2639243594
2.7489-2.83760.27321460.2582265596
2.8376-2.93910.3231450.261269297
2.9391-3.05670.2981360.267267296
3.0567-3.19590.32831440.2601270397
3.1959-3.36440.32781500.2434274698
3.3644-3.57520.28991490.2389271798
3.5752-3.85120.2521280.2062237185
3.8512-4.23880.25451390.2023257892
4.2388-4.85210.2121500.1853278599
4.8521-6.1130.27721510.2261281499
6.113-92.2310.2421500.209280495
Refinement TLS params.Method: refined / Origin x: 16.3111 Å / Origin y: 28.2205 Å / Origin z: 28.4471 Å
111213212223313233
T0.0481 Å20.0009 Å20.0019 Å2-0.0161 Å20.0047 Å2--0.0544 Å2
L0.0989 °20.0169 °20.0833 °2-0.0195 °2-0.0276 °2--0.2412 °2
S-0.0312 Å °0.0193 Å °-0.023 Å °0.0053 Å °0.0089 Å °0.012 Å °-0.0246 Å °0.0325 Å °-0.0157 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-3 - 275
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allB-3 - 275
4X-RAY DIFFRACTION1allB301
5X-RAY DIFFRACTION1allC-3 - 275
6X-RAY DIFFRACTION1allC301
7X-RAY DIFFRACTION1allD-3 - 274
8X-RAY DIFFRACTION1allD301
9X-RAY DIFFRACTION1allS1 - 239

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