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- PDB-3h16: Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus... -

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Basic information

Entry
Database: PDB / ID: 3h16
TitleCrystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans
ComponentsTIR protein
KeywordsSIGNALING PROTEIN / Bacteria TIR domain
Function / homology
Function and homology information


NADP+ nucleosidase activity / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / signal transduction
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
NAD(+) hydrolase PdTIR
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsChan, S.L. / Low, L.Y. / Santelli, E. / Pascual, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Molecular Mimicry in Innate Immunity: CRYSTAL STRUCTURE OF A BACTERIAL TIR DOMAIN.
Authors: Chan, S.L. / Low, L.Y. / Hsu, S. / Li, S. / Liu, T. / Santelli, E. / Le Negrate, G. / Reed, J.C. / Woods, V.L. / Pascual, J.
History
DepositionApr 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIR protein
B: TIR protein
C: TIR protein
D: TIR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3215
Polymers68,2254
Non-polymers961
Water1,02757
1
A: TIR protein
B: TIR protein


Theoretical massNumber of molelcules
Total (without water)34,1122
Polymers34,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-8 kcal/mol
Surface area13160 Å2
MethodPISA
2
C: TIR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1522
Polymers17,0561
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: TIR protein


Theoretical massNumber of molelcules
Total (without water)17,0561
Polymers17,0561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.780, 85.610, 89.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
TIR protein


Mass: 17056.229 Da / Num. of mol.: 4 / Fragment: residues 146-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans PD1222 (bacteria)
Gene: Pden_0113, PdTLP / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: A1AY86
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium cacodylate pH 6.0, 31% PEG 8000 and 0.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1981
2981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.979, 0.980, 0.855
SYNCHROTRONSSRL BL9-220.979
Detector
IDDate
1May 20, 2008
2Aug 5, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorMADMx-ray1
2Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.981
30.8551
ReflectionRedundancy: 2 % / Av σ(I) over netI: 23.71 / Number: 92178 / Rmerge(I) obs: 0.068 / Χ2: 1.18 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 46868 / % possible obs: 88
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955099.810.0291.1622
3.934.9510010.0381.1792
3.443.9399.810.0561.0892
3.123.4410010.0791.2072
2.93.1299.810.1241.172
2.732.996.910.1771.2172
2.592.7385.310.2251.2461.9
2.482.5973.910.2421.2071.9
2.382.4865.210.2871.1751.8
2.32.3859.110.3181.21.7
ReflectionResolution: 2.5→50 Å / Num. obs: 20938 / % possible obs: 95.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.711
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.5-2.593.50.19278.8
2.59-2.693.60.18385.6
2.69-2.823.70.16492.8
2.82-2.963.80.14997.5
2.96-3.1540.11999.2
3.15-3.394.10.085100
3.39-3.734.10.064100
3.73-4.274.10.047100
4.27-5.3840.035100
5.38-503.80.02899.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→8 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1684
RfactorNum. reflection% reflection
Rfree0.243 1725 8.1 %
Rwork0.192 --
obs0.192 17535 82.1 %
all-21351 -
Solvent computationBsol: 54.858 Å2
Displacement parametersBiso mean: 40.611 Å2
Baniso -1Baniso -2Baniso -3
1-23.597 Å20 Å20 Å2
2---12.203 Å20 Å2
3----11.394 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4229 0 5 57 4291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.237
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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