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- PDB-4lzp: Structure of the TIR domain of the immunosuppressor BtpA from Brucella -

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Basic information

Entry
Database: PDB / ID: 4lzp
TitleStructure of the TIR domain of the immunosuppressor BtpA from Brucella
ComponentsPutative uncharacterized protein
KeywordsIMMUNE SYSTEM / TIR domain / Virulence factor Immuno suppressor / MyD88 / membrane
Function / homology
Function and homology information


NAD+ catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / lipid binding / host cell plasma membrane / signal transduction / extracellular region / membrane
Similarity search - Function
Toll/interleukin-1 receptor homology (TIR) domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable 2' cyclic ADP-D-ribose synthase TcpB
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsKaplan-turkoz, B. / O'callaghan, D. / Vergunst, A. / Terradot, L.
CitationJournal: Febs Lett. / Year: 2013
Title: Structure of the Toll/interleukin 1 receptor (TIR) domain of the immunosuppressive Brucella effector BtpA/Btp1/TcpB
Authors: Kaplan-turkoz, B. / Koelblen, T. / Felix, C. / Candusso, M.P. / O'callaghan, D. / Vergunst, A.C. / Terradot, L.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
B: Putative uncharacterized protein
C: Putative uncharacterized protein
A: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)79,8074
Polymers79,8074
Non-polymers00
Water00
1
B: Putative uncharacterized protein
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)39,9032
Polymers39,9032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-11 kcal/mol
Surface area13650 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)39,9032
Polymers39,9032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-9 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.143, 73.928, 137.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
Putative uncharacterized protein


Mass: 19951.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: ATCC 23457 / Gene: BMEA_A0279 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C0RGW8

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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: 2.17 Å3/Da / Density % sol: 43.37 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 20% Peg4K, 100mM Na Acetate, 200mM ammonium acetate, pH 5.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.15→48.4 Å / Num. obs: 43030 / % possible obs: 98.1 % / Observed criterion σ(F): 1.1 / Observed criterion σ(I): 1.1 / Rmerge(I) obs: 0.169
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3.15-3.323.60.6681.51768199.2
3.32-3.523.60.472.21683198.4
3.52-3.763.60.343.11574199.1
3.76-4.073.50.2014.51486198.6
4.07-4.453.60.1456.11340198.1
4.45-4.983.50.1028.21235197.8
4.98-5.753.50.1067.41096197.5
5.75-7.043.40.1047.4921196.9
7.04-9.963.50.05211.4727196.4
9.96-48.423.20.03513.7421193.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H16

3h16


Resolution: 3.15→48.4 Å / SU ML: 0.45 / σ(F): 0.09 / Phase error: 30.8 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2787 1083 4.76 %
Rwork0.2224 --
obs0.2252 22751 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4669 0 0 0 4669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094752
X-RAY DIFFRACTIONf_angle_d0.9926403
X-RAY DIFFRACTIONf_dihedral_angle_d14.3721737
X-RAY DIFFRACTIONf_chiral_restr0.051724
X-RAY DIFFRACTIONf_plane_restr0.006809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.15-3.29370.38291600.3304272499
3.2937-3.46730.37021150.3023276999
3.4673-3.68440.36871280.2795270698
3.6844-3.96880.32061270.2412275199
3.9688-4.3680.25451430.2092269698
4.368-4.99940.22161320.1717272098
4.9994-6.29660.20551400.1865269097
6.2966-48.42850.23581380.1639261295
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)
13.78751.2726-0.25626.2234-0.16975.5314-0.06430.01730.57110.27090.42510.78040.0326-1.144-0.33590.3937-0.13250.07660.69730.00950.642631.894-0.005-56.983
23.03271.9169-0.67853.9844-0.93461.36-0.15980.05310.31720.1701-0.10930.3494-0.1799-0.48280.38230.7005-0.20160.03830.6512-0.3130.683533.8780.36-58.176
32.0212.8387-6.2652.0083-3.11652.01680.3869-1.0239-0.75910.6353-0.1171-0.41110.2932-0.3206-0.15680.6651-0.0341-0.0590.57210.09630.690223.47-5.912-66.021
43.88520.6881-0.31934.41381.28193.2590.220.6893-0.38360.2206-0.31920.8059-0.2819-0.57820.12410.3555-0.0099-0.03880.6693-0.11080.443422.796-2.639-53.751
52.0019.02022.6458.8164-3.16544.30630.1109-0.6109-0.31080.8634-0.0231-0.41990.31350.15730.01980.567-0.1343-0.04160.2341-0.03860.906315.004-9.03-56.463
60.65080.0984-0.91080.44380.17171.15160.2239-1.321-0.49130.66790.0908-0.81420.26020.99460.00961.0287-0.122-0.2034-2.1682-0.40230.723726.517-12.262-54.804
74.52532.60.05583.20621.01833.9861-0.04960.5767-0.5566-0.28050.2566-0.72860.08790.4456-0.18390.3874-0.0432-0.09630.5559-0.20010.592817.729-7.737-44.053
82.491-1.6237-2.52854.4832-0.50663.9756-0.8521-0.0311-0.39780.1335-0.0968-1.0190.05470.7950.94210.38450.0353-0.01540.71660.2030.595130.27-10.479-44.389
93.88130.25981.70278.0405-3.20867.58710.2901-0.3499-0.52170.34740.01890.43020.5196-0.7808-0.32320.5799-0.06190.05430.65040.07460.82539.882-10.939-51.245
100.1032-0.0545-0.33710.07540.26651.1585-0.2212-0.35270.27751.4140.43630.1321-0.4756-0.3786-0.28250.9814-0.0670.051.234-0.10160.469417.507-7.723-12.5
115.54-0.6833-1.39411.3585-1.94445.25340.4787-0.2711-1.1376-0.3595-0.17790.14320.8558-0.0985-0.38760.6358-0.0126-0.16070.53150.0360.508519.9411.405-26.047
127.29922.3357-1.19052.0644-0.26021.3670.4264-1.6188-1.21950.5515-0.2637-0.13180.4404-0.1398-0.22070.4467-0.0782-0.10710.49470.15310.678117.616-0.858-21.501
131.99021.35226.4575.83.21795.10810.5571-1.186-0.59240.7883-0.06041.31390.2284-1.2091-0.20310.6094-0.04540.09511.41240.0670.521228.559-0.474-13.593
144.1449-1.4693-1.13441.9318-1.65053.36330.10320.558-0.0607-0.168-0.04310.33920.5646-0.431-0.11240.3742-0.0461-0.09390.54030.190.407127.40.573-28.25
157.2437-3.59950.19192.01440.99065.23540.0073-0.4857-0.21921.0289-0.07880.7605-0.1963-0.4120.0560.6888-0.14120.0141.51480.1670.477536.7475.038-24.662
164.60320.20581.58821.864-1.26674.1544-0.6134-0.52560.66530.17230.07570.4485-0.3498-0.81060.48950.36770.10390.02860.7133-0.0050.440730.845-6.306-26.077
172.02710.89381.68331.89120.43792.00480.2267-0.62120.7526-0.29250.52980.3787-0.0329-0.1358-0.39430.48510.09220.02710.6595-0.03910.501538.161-1.695-34.823
181.83342.1645-0.27893.604-0.30394.48460.12060.04730.07050.5143-0.2110.14140.09910.10390.06530.4689-0.1907-0.18560.42060.24520.81526.421-10.654-33.645
198.56692.22191.5112.03034.31911.9988-0.06130.60130.4689-0.55670.9443-0.38570.2814-0.0656-0.42950.60380.0289-0.10280.44870.21030.386918.679-14.677-25.955
203.9026-0.6096-3.70922.67680.58822.027-0.2530.3821-1.11960.2927-0.3760.06120.0105-0.23380.28540.5003-0.0784-0.05280.5984-0.01640.6593-2.38817.597-31.939
215.13880.4481-1.4183.9002-1.96654.7464-0.2468-0.11320.5836-1.11360.5162-0.78060.36040.1136-0.31440.5954-0.10990.07580.9418-0.12750.6362-1.4592.341-8.357
224.3489-0.8094-0.82626.35641.6123.7591-0.58710.31390.584-0.9935-0.26730.4038-1.2241-0.39160.72970.73730.2261-0.1481.5394-0.00420.69032.449-2.895-13.607
235.3478-0.8863-1.73484.31361.21257.7630.15730.48230.4485-0.81210.5149-0.7593-0.6502-0.6679-0.45850.5662-0.0628-0.06080.4640.13390.7124-10.6280.431-10.845
246.02380.0005-3.24250.0996-0.47253.8438-0.2199-0.2915-0.2388-0.27590.30690.21680.2279-0.973-0.12910.4708-0.0096-0.10090.8677-0.16940.6674-16.5726.798-12.119
254.1237-1.3226-1.46652.45621.14393.42950.26670.0154-0.2743-0.2118-0.31660.2403-0.042-0.23740.1290.48550.0253-0.14890.4427-0.16130.5561-6.5967.301-22.51
265.4881-1.38561.50014.01460.57810.65710.3181.4747-0.3098-1.01870.00420.2150.0009-0.0950.02110.65310.2604-0.16711.06-0.39550.7689-13.7274.198-55.167
273.8469-2.7969-1.39747.9126-1.56793.0502-0.442-0.5712-0.62040.6109-0.24410.5520.1304-1.1060.40670.58320.1417-0.09620.787-0.21780.6301-15.205-6.092-40.397
282.665-2.9858-0.08854.9514-0.53261.83940.32950.7003-0.3786-0.88510.11150.2245-0.0602-1.55620.00950.5661-0.0004-0.27270.7404-0.2070.7847-16.33-1.143-47.995
292.8146-1.14790.88354.05050.65643.95890.36741.2406-0.1231-1.3943-0.6198-0.2258-0.2935-0.01450.16970.98920.2773-0.11550.7645-0.20980.5469-6.254-0.349-53.114
304.978-0.75810.6596.86421.7150.861-0.56120.0359-0.63010.4260.09340.23240.52690.03760.2510.47040.0121-0.09440.3321-0.12650.5285-3.375-8.631-39.55
311.9972-8.3968-2.95178.0806-2.62658.83880.21480.20920.1647-0.30790.0039-0.1366-0.7451-0.07380.07740.4292-0.0019-0.03760.8692-0.07380.60084.486-2.555-46.76
321.6334-1.66012.32073.64450.28967.08340.3774-0.41550.6555-0.811-0.5436-0.619-0.35960.64380.24870.3808-0.19890.04620.8571-0.16170.738-3.3155.84-46.406
333.3023-4.4397-1.50672.08331.37872.07030.094-1.0184-0.20760.57440.7660.04220.26070.2273-0.98980.590.0585-0.00930.517-0.02680.5986-0.002-1.566-32.487
344.9123-1.28911.83494.058-1.45731.2454-0.6364-0.12810.4729-0.57790.1857-0.74720.0865-0.3180.33070.43270.01190.01180.3677-0.0630.423-2.9776.446-36.89
359.18561.4533-3.51852.0145-2.10262.007-0.03350.25340.6216-0.0038-0.04210.0797-0.8219-0.1352-0.05060.7566-0.0577-0.18010.395-0.04830.4345-15.05712.614-43.703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 143 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 196 )
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 214 )
5X-RAY DIFFRACTION5chain 'A' and (resid 215 through 221 )
6X-RAY DIFFRACTION6chain 'A' and (resid 222 through 236 )
7X-RAY DIFFRACTION7chain 'A' and (resid 237 through 253 )
8X-RAY DIFFRACTION8chain 'A' and (resid 254 through 263 )
9X-RAY DIFFRACTION9chain 'A' and (resid 264 through 275 )
10X-RAY DIFFRACTION10chain 'B' and (resid 143 through 145 )
11X-RAY DIFFRACTION11chain 'B' and (resid 146 through 158 )
12X-RAY DIFFRACTION12chain 'B' and (resid 159 through 185 )
13X-RAY DIFFRACTION13chain 'B' and (resid 186 through 198 )
14X-RAY DIFFRACTION14chain 'B' and (resid 199 through 210 )
15X-RAY DIFFRACTION15chain 'B' and (resid 211 through 220 )
16X-RAY DIFFRACTION16chain 'B' and (resid 221 through 240 )
17X-RAY DIFFRACTION17chain 'B' and (resid 241 through 253 )
18X-RAY DIFFRACTION18chain 'B' and (resid 254 through 263 )
19X-RAY DIFFRACTION19chain 'B' and (resid 264 through 275 )
20X-RAY DIFFRACTION20chain 'C' and (resid 100 through 132 )
21X-RAY DIFFRACTION21chain 'C' and (resid 133 through 153 )
22X-RAY DIFFRACTION22chain 'C' and (resid 154 through 179 )
23X-RAY DIFFRACTION23chain 'C' and (resid 180 through 211 )
24X-RAY DIFFRACTION24chain 'C' and (resid 212 through 231 )
25X-RAY DIFFRACTION25chain 'C' and (resid 232 through 275 )
26X-RAY DIFFRACTION26chain 'D' and (resid 141 through 149 )
27X-RAY DIFFRACTION27chain 'D' and (resid 150 through 158 )
28X-RAY DIFFRACTION28chain 'D' and (resid 159 through 185 )
29X-RAY DIFFRACTION29chain 'D' and (resid 186 through 204 )
30X-RAY DIFFRACTION30chain 'D' and (resid 205 through 214 )
31X-RAY DIFFRACTION31chain 'D' and (resid 215 through 222 )
32X-RAY DIFFRACTION32chain 'D' and (resid 223 through 236 )
33X-RAY DIFFRACTION33chain 'D' and (resid 237 through 247 )
34X-RAY DIFFRACTION34chain 'D' and (resid 248 through 263 )
35X-RAY DIFFRACTION35chain 'D' and (resid 264 through 275 )

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