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- PDB-7bxf: MvcA-Lpg2149 complex -

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Basic information

Entry
Database: PDB / ID: 7bxf
TitleMvcA-Lpg2149 complex
Components
  • Lpg2149
  • MvcA
KeywordsTRANSFERASE / ubiquitination / deubiquitination / MavC / MvcA / Lpg2149 / UBE2N
Function / homology: / MvcA insertion domain / PRASEODYMIUM ION / 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.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
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 / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
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: MvcA
C: Lpg2149
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1076
Polymers58,5442
Non-polymers5644
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-35 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.998, 81.229, 54.253
Angle α, β, γ (deg.)90.000, 95.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MvcA


Mass: 45921.230 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: lpg2148 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTL3
#2: Protein Lpg2149


Mass: 12622.402 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
#3: Chemical
ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 2% Tacsimate, pH 4.0, 0.1 M 426 sodium acecate, pH 4.6, 16% PEG3350

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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: Oct 11, 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: 15703 / % possible obs: 96.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.6
Reflection shellResolution: 2.7→2.76 Å / Num. unique obs: 1071 / CC1/2: 0.944

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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: 5SUJ,5DPO

5suj

5dpo


Resolution: 2.7→24.821 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 824 5.25 %
Rwork0.2143 14878 -
obs0.2166 15702 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.53 Å2 / Biso mean: 49.6244 Å2 / Biso min: 10.84 Å2
Refinement stepCycle: final / Resolution: 2.7→24.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 4 62 3881
Biso mean--44.15 30.62 -
Num. residues----473
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.8690.31591300.2727240994
2.869-3.09010.32671550.2548245997
3.0901-3.40040.33061300.251248296
3.4004-3.89080.28481470.2136251197
3.8908-4.89580.19611430.1837248696
4.8958-24.820.20311190.1867253195
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)
12.50390.5248-0.27570.2182-0.1162.32980.089-0.05360.26130.2283-0.01320.107-0.5061-0.1377-0.04480.26820.0670.01140.1301-0.01930.204251.43914.659524.8758
23.3905-1.41131.91650.7-0.59161.34110.08510.37380.0771-0.283-0.14380.03990.2444-0.04790.10540.3306-0.0593-0.05980.3933-0.05390.348926.8499-5.647110.802
33.1011-0.23831.74180.4107-0.34891.66690.0176-0.1591-0.0272-0.09660.00820.3197-0.0046-0.4084-0.06120.24930.0330.00820.3261-0.06180.397921.7933-0.109920.2971
42.44810.71290.34150.95590.1841.2383-0.0495-0.2120.0329-0.18960.0081-0.005-0.03130.00830.03330.26480.053-0.00990.12030.01070.109148.9338-1.715426.7106
51.2790.24330.2233.4216-1.23494.0096-0.0617-0.13470.182-0.4520.42510.4825-0.1685-0.6892-0.150.22120.08190.02650.2285-0.01540.247748.67311.493810.0488
63.4017-3.2518-0.29723.13580.24330.0853-0.11210.70920.3421-0.99710.20350.818-0.52590.1195-0.08760.6385-0.0235-0.14310.38390.12430.353946.75153.1165-5.6653
73.5272-0.21491.35443.8514-0.10534.43090.16490.2002-0.0637-0.40040.06180.3241-0.0646-0.1471-0.06290.21920.01890.05430.2154-0.0080.242554.2241-0.91232.736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 82 )A13 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 187 )A83 - 187
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 316 )A188 - 316
4X-RAY DIFFRACTION4chain 'A' and (resid 317 through 395 )A317 - 395
5X-RAY DIFFRACTION5chain 'C' and (resid 11 through 43 )C11 - 43
6X-RAY DIFFRACTION6chain 'C' and (resid 44 through 54 )C44 - 54
7X-RAY DIFFRACTION7chain 'C' and (resid 55 through 114 )C55 - 114

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