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- PDB-5miy: Crystal structure of the E3 ubiquitin ligase RavN from Legionella... -

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Basic information

Entry
Database: PDB / ID: 5miy
TitleCrystal structure of the E3 ubiquitin ligase RavN from Legionella pneumophila
ComponentsE3 ubiquitin ligase RavN
KeywordsLIGASE / Legionella effector / E3 ubiquitin ligase / UNKNOWN FUNCTION
Function / homologyUncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.717 Å
AuthorsLucas, M. / Abascal-Palacios, G. / Rojas, A.L. / Hierro, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-59759-R Spain
CitationJournal: PLoS Pathog. / Year: 2018
Title: RavN is a member of a previously unrecognized group of Legionella pneumophila E3 ubiquitin ligases.
Authors: Lin, Y.H. / Lucas, M. / Evans, T.R. / Abascal-Palacios, G. / Doms, A.G. / Beauchene, N.A. / Rojas, A.L. / Hierro, A. / Machner, M.P.
History
DepositionNov 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin ligase RavN
B: E3 ubiquitin ligase RavN
C: E3 ubiquitin ligase RavN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,30825
Polymers43,6573
Non-polymers1,65122
Water4,270237
1
A: E3 ubiquitin ligase RavN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1079
Polymers14,5521
Non-polymers5548
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin ligase RavN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1578
Polymers14,5521
Non-polymers6047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin ligase RavN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0458
Polymers14,5521
Non-polymers4927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.160, 177.010, 79.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-388-

HOH

21B-391-

HOH

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Components

#1: Protein E3 ubiquitin ligase RavN


Mass: 14552.272 Da / Num. of mol.: 3 / Fragment: Residues 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: ERS253249_02460 / Plasmid: pGST-Parallel2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A130MLL2, ubiquitin-protein ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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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: 4.6 Å3/Da / Density % sol: 73.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1.5 M Ammonium sulphate, 0.1 M NaCitrate pH 5.4 and 0.2 M K/Na Tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97887 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 1.72→47.969 Å / Num. obs: 85768 / % possible obs: 99.7 % / Redundancy: 13.228 % / Biso Wilson estimate: 31.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.057 / Χ2: 1.065 / Net I/σ(I): 24.57 / Num. measured all: 1134512
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.72-1.8212.7410.8743.1417248413730135380.7190.9198.6
1.82-1.9513.3470.6394.8617295312959129580.9260.664100
1.95-2.113.5270.3569.1516347012085120850.9850.37100
2.1-2.313.4740.19415.9214978711117111170.9950.201100
2.3-2.5713.4810.11125.2113647010124101230.9980.115100
2.57-2.9713.4710.06439.08120392893789370.9990.067100
2.97-3.6313.3380.04157.91101545761476130.9990.042100
3.63-5.1212.6650.03470.7975409595559540.9990.035100
5.12-47.96912.1990.03271.8442002346634430.9990.03399.3

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XSCALEdata scaling
SHELXphasing
PDB_EXTRACT3.2data extraction
XSCALEdata reduction
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.717→46.357 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1949 4287 5 %
Rwork0.1607 81455 -
obs0.1624 85742 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.85 Å2 / Biso mean: 48.0344 Å2 / Biso min: 21.98 Å2
Refinement stepCycle: final / Resolution: 1.717→46.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 89 237 3323
Biso mean--69.03 57.19 -
Num. residues----372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.717-1.73610.37111330.34082529266293
1.7361-1.75660.30791410.296226632804100
1.7566-1.7780.29721410.278926792820100
1.778-1.80050.29651410.26126972838100
1.8005-1.82420.31271410.239426742815100
1.8242-1.84920.30361450.225827492894100
1.8492-1.87560.26531400.221926662806100
1.8756-1.90360.22341430.196827082851100
1.9036-1.93330.22471410.192126872828100
1.9333-1.9650.22921440.176427202864100
1.965-1.99890.19661400.173626882828100
1.9989-2.03530.2171430.174727112854100
2.0353-2.07440.21161410.158226762817100
2.0744-2.11670.1871420.147327122854100
2.1167-2.16280.17851440.148727352879100
2.1628-2.21310.171420.150726872829100
2.2131-2.26840.19211430.158727172860100
2.2684-2.32980.21891420.159427042846100
2.3298-2.39830.21111440.161327382882100
2.3983-2.47570.20931430.1627102853100
2.4757-2.56420.23321430.169827082851100
2.5642-2.66690.19431420.153427132855100
2.6669-2.78820.19211440.171727302874100
2.7882-2.93520.20081450.166727612906100
2.9352-3.11910.21391430.185427182861100
3.1191-3.35980.20351450.160327512896100
3.3598-3.69780.1811450.149627462891100
3.6978-4.23260.14531470.135527952942100
4.2326-5.33130.17721470.131827912938100
5.3313-46.37360.18191520.15812892304499

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