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- PDB-6l6h: Crystal structure of Lpg0189 -

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Basic information

Entry
Database: PDB / ID: 6l6h
TitleCrystal structure of Lpg0189
ComponentsUncharacterized protein Lpg0189
KeywordsUNKNOWN FUNCTION / Lpg0189 / Legionella pneumophila / novel fold / T2SS effector
Function / homology: / T2SS substrate NttE / ACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsGe, H. / Chen, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31970103 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of a hypothetical T2SS effector Lpg0189 from Legionella pneumophila reveals a novel protein fold.
Authors: Chen, X. / Liu, S. / Jiang, S. / Zhang, X. / Zhang, N. / Ma, J. / Ge, H.
History
DepositionOct 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Lpg0189
B: Uncharacterized protein Lpg0189
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9114
Polymers62,7602
Non-polymers1512
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-9 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.758, 122.758, 104.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-443-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 25 through 55 or resid 57...
21(chain B and (resid 25 through 55 or resid 57...

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
11THRTHRGLNGLN(chain A and (resid 25 through 55 or resid 57...AA25 - 556 - 36
12ALAALAPHEPHE(chain A and (resid 25 through 55 or resid 57...AA57 - 10138 - 82
13TYRTYRVALVAL(chain A and (resid 25 through 55 or resid 57...AA103 - 25884 - 239
14GLUGLULEULEU(chain A and (resid 25 through 55 or resid 57...AA260 - 288241 - 269
21THRTHRGLNGLN(chain B and (resid 25 through 55 or resid 57...BB25 - 556 - 36
22ALAALAPHEPHE(chain B and (resid 25 through 55 or resid 57...BB57 - 10138 - 82
23TYRTYRVALVAL(chain B and (resid 25 through 55 or resid 57...BB103 - 25884 - 239
24GLUGLULEULEU(chain B and (resid 25 through 55 or resid 57...BB260 - 288241 - 269

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Components

#1: Protein Uncharacterized protein Lpg0189


Mass: 31379.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Gene: lpg0189 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZZ22
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.63 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.4M Ammonium citrate dibasic, 0.1M Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 34257 / % possible obs: 95.7 % / Redundancy: 10.5 % / CC1/2: 0.99 / Net I/σ(I): 19.1
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 3505 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L6G

6l6g


Resolution: 2.403→29.451 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.85
RfactorNum. reflection% reflection
Rfree0.2284 1502 5.04 %
Rwork0.1795 --
obs0.182 29831 83.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.93 Å2 / Biso mean: 43.4932 Å2 / Biso min: 16.78 Å2
Refinement stepCycle: final / Resolution: 2.403→29.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 10 205 4559
Biso mean--58.56 43.18 -
Num. residues----528
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1562X-RAY DIFFRACTION3.872TORSIONAL
12B1562X-RAY DIFFRACTION3.872TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.403-2.48010.2375760.1929139046
2.4801-2.56870.2404860.2061165854
2.5687-2.67140.27661200.222211569
2.6714-2.79290.28981460.2172284693
2.7929-2.94010.25311750.2123051100
2.9401-3.12410.28381660.20023071100
3.1241-3.3650.23791510.19773100100
3.365-3.7030.30061230.204235876
3.703-4.23750.19591340.154235876
4.2375-5.33360.17131570.13173151100
5.3336-29.4510.19581680.1759323199
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)
10.6444-0.6003-0.58041.9117-0.72774.2720.0112-0.087-0.0048-0.0669-0.0399-0.16440.06140.6919-0.05730.2657-0.17450.01730.6266-0.06660.364349.6947167.1034114.0842
21.24180.2291-0.48730.3915-1.2813.4442-0.02280.10680.0220.2051-0.17110.0162-0.41660.52230.16130.2914-0.15860.03030.3671-0.0110.291148.2784177.2357102.6716
32.30740.39430.49273.17980.89893.53860.3094-0.4436-0.38430.4794-0.0738-0.31450.6840.6161-0.15310.3236-0.0114-0.09650.46720.09820.309342.7347153.3156120.6196
40.92550.3796-1.82050.18950.04893.7472-0.2799-0.078-0.1830.0740.1123-0.18370.8421-0.21490.21430.519-0.1249-0.00330.2858-0.00170.327915.8052147.5637111.6595
50.2086-0.5136-0.63550.8458-0.17735.54050.07050.0793-0.05110.04250.13460.17140.1784-1.3704-0.14280.193-0.17120.01760.5470.06430.28037.712152.5795123.9744
61.7408-0.0646-0.48570.70390.55463.31630.0475-0.1302-0.23550.1798-0.0258-0.0360.72120.0944-0.00050.3057-0.0434-0.00850.20450.05340.269231.5217148.4091103.8311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 65 )A25 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 164 )A66 - 164
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 288 )A165 - 288
4X-RAY DIFFRACTION4chain 'B' and (resid 25 through 65 )B25 - 65
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 164 )B66 - 164
6X-RAY DIFFRACTION6chain 'B' and (resid 165 through 288 )B165 - 288

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