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- PDB-7bxh: MavC-Lpg2149 complex -

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Basic information

Entry
Database: PDB / ID: 7bxh
TitleMavC-Lpg2149 complex
Components
  • Lpg2149
  • MavC
KeywordsTRANSFERASE / ubiquitination / deubiquitination / MavC / MvcA / Lpg2149 / UBE2N
Function / homology: / MvcA insertion domain / Uncharacterized protein / MvcA insertion domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGao, P. / Wang, Y.
CitationJournal: Nat Commun / Year: 2020
Title: Insights into catalysis and regulation of non-canonical ubiquitination and deubiquitination by bacterial deamidase effectors.
Authors: Wang, Y. / Zhan, Q. / Wang, X. / Li, P. / Liu, S. / Gao, G. / Gao, P.
History
DepositionApr 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lpg2149
B: MavC


Theoretical massNumber of molelcules
Total (without water)56,3652
Polymers56,3652
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-10 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.651, 62.817, 138.391
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lpg2149


Mass: 12365.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg2149 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTL2
#2: Protein MavC


Mass: 43999.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg2147 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTL4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M sodium acetate, pH 4.0, 10% PEG4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14489 / % possible obs: 99.8 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.76 Å / Rmerge(I) obs: 0.524 / Num. unique obs: 14489

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSC,5DPO

5tsc

5dpo


Resolution: 2.7→37.182 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 741 5.11 %
Rwork0.2053 13748 -
obs0.2079 14489 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.93 Å2 / Biso mean: 42.5983 Å2 / Biso min: 11.73 Å2
Refinement stepCycle: final / Resolution: 2.7→37.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3859 0 0 49 3908
Biso mean---30.7 -
Num. residues----478
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.90840.31711400.2572262796
2.9084-3.20090.33961420.252711100
3.2009-3.66380.26751750.21672717100
3.6638-4.61460.22391340.17932784100
4.6146-37.180.21741500.1857290999
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)
11.7692-1.34141.07793.6772-0.90640.44880.09340.1666-0.228-0.1265-0.0126-0.02910.1947-0.12310.00240.24510.00690.01410.2324-0.08970.379916.8009-19.6751-22.076
22.1863-0.9996-0.03532.10470.33130.99090.04280.21780.1828-0.2470.1385-0.3-0.13830.0575-0.1080.2786-0.02640.03860.2915-0.09920.231613.84292.8031-26.639
33.43740.0282-1.5072.4135-0.14873.9368-0.0293-0.2182-0.17350.0842-0.1531-0.0017-0.16240.0990.10390.1926-0.0505-0.01550.12780.00270.2475.063414.80518.3662
42.1938-0.1538-0.32343.65171.15712.6431-0.08740.33550.0488-0.1111-0.00240.1691-0.0946-0.1313-0.0020.19790.0775-0.01660.3447-0.0250.19231.65492.1761-26.1389
51.6675-1.2920.33363.24210.00321.1960.13640.1698-0.23-0.37860.0532-0.27890.02080.0495-0.08750.2133-0.02970.01340.2787-0.06650.257716.7373-13.7507-26.2505
62.83940.52830.25732.9579-0.78954.31950.037-0.2501-0.24590.431-0.1856-0.4462-0.1621-0.2653-0.06550.3473-0.0501-0.05420.2861-0.03970.414227.7584-8.4841-8.798
76.614-0.4179-0.14914.20320.07792.6598-0.1103-1.1848-0.63311.0936-0.0493-2.13410.23271.19330.31890.64640.1333-0.20230.79530.09051.164340.6859-12.0613-3.1409
84.48923.5269-2.70753.2253-0.85395.0728-0.2851.041-1.0877-0.04770.147-1.04420.76040.29090.16610.3450.0435-0.18280.4618-0.15840.638435.8892-17.7451-10.3343
93.2557-0.2230.7585.32380.91774.8712-0.03590.36770.24820.21810.2986-0.3645-0.5610.2473-0.29270.2876-0.0321-0.05640.4501-0.00170.478132.9518-7.3011-12.5738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 7 through 63 )B7 - 63
2X-RAY DIFFRACTION2chain 'B' and (resid 64 through 127 )B64 - 127
3X-RAY DIFFRACTION3chain 'B' and (resid 128 through 222 )B128 - 222
4X-RAY DIFFRACTION4chain 'B' and (resid 223 through 315 )B223 - 315
5X-RAY DIFFRACTION5chain 'B' and (resid 316 through 382 )B316 - 382
6X-RAY DIFFRACTION6chain 'A' and (resid 11 through 54 )A11 - 54
7X-RAY DIFFRACTION7chain 'A' and (resid 55 through 69 )A55 - 69
8X-RAY DIFFRACTION8chain 'A' and (resid 70 through 82 )A70 - 82
9X-RAY DIFFRACTION9chain 'A' and (resid 83 through 112 )A83 - 112

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