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- PDB-4c7m: The crystal structure of TcpB or BtpA TIR domain -

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Basic information

Entry
Database: PDB / ID: 4c7m
TitleThe crystal structure of TcpB or BtpA TIR domain
ComponentsToll/interleukin-1 receptor domain-containing protein
KeywordsSIGNALING PROTEIN / PROTEIN
Function / homology
Function and homology information


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
Toll/interleukin-1 receptor domain-containing protein
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsAlaidarous, M. / Ve, T. / Casey, L.W. / Valkov, E. / Ullah, M.O. / Schembri, M.A. / Mansell, A. / Sweet, M.J. / Kobe, B.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Mechanism of bacterial interference with TLR4 signaling by Brucella Toll/interleukin-1 receptor domain-containing protein TcpB.
Authors: Alaidarous, M. / Ve, T. / Casey, L.W. / Valkov, E. / Ericsson, D.J. / Ullah, M.O. / Schembri, M.A. / Mansell, A. / Sweet, M.J. / Kobe, B.
History
DepositionSep 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / exptl_crystal_grow / pdbx_database_status / reflns / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Dec 20, 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

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Assembly

Deposited unit
A: Toll/interleukin-1 receptor domain-containing protein
B: Toll/interleukin-1 receptor domain-containing protein
C: Toll/interleukin-1 receptor domain-containing protein
D: Toll/interleukin-1 receptor domain-containing protein


Theoretical massNumber of molelcules
Total (without water)60,2404
Polymers60,2404
Non-polymers00
Water1448
1
A: Toll/interleukin-1 receptor domain-containing protein


Theoretical massNumber of molelcules
Total (without water)15,0601
Polymers15,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Toll/interleukin-1 receptor domain-containing protein


Theoretical massNumber of molelcules
Total (without water)15,0601
Polymers15,0601
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Toll/interleukin-1 receptor domain-containing protein


Theoretical massNumber of molelcules
Total (without water)15,0601
Polymers15,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Toll/interleukin-1 receptor domain-containing protein


Theoretical massNumber of molelcules
Total (without water)15,0601
Polymers15,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.966, 73.676, 74.759
Angle α, β, γ (deg.)90.00, 93.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Toll/interleukin-1 receptor domain-containing protein


Mass: 15060.121 Da / Num. of mol.: 4 / Fragment: TIR DOMAIN, RESIDUES 90-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: EXD79_08750 / Plasmid: PMCSG7 VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A4P6KMT3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.5 Å3/Da / Density % sol: 50.7 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS PH 5.5, 0.2 M NACL, 25%(W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953693
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953693 Å / Relative weight: 1
ReflectionResolution: 2.6→42.42 Å / Num. obs: 18090 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 63.53 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 1.9
Reflection shellResolution: 2.6→42.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H16
Resolution: 2.57→42.42 Å / Cor.coef. Fo:Fc: 0.9155 / Cor.coef. Fo:Fc free: 0.8999 / SU R Cruickshank DPI: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.715 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.293 / Details: DISORDERED REGION WITH NO DENSITY WERE NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 1009 5.58 %RANDOM
Rwork0.2317 ---
obs0.2322 18079 99.9 %-
Displacement parametersBiso mean: 59.46 Å2
Baniso -1Baniso -2Baniso -3
1-5.965 Å20 Å27.2796 Å2
2---0.9446 Å20 Å2
3----5.0204 Å2
Refine analyzeLuzzati coordinate error obs: 0.411 Å
Refinement stepCycle: LAST / Resolution: 2.57→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 0 8 4069
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014137HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055574HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1461SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes595HARMONIC5
X-RAY DIFFRACTIONt_it4137HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion16.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion537SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4377SEMIHARMONIC4
LS refinement shellResolution: 2.57→2.73 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2833 151 5.19 %
Rwork0.2601 2756 -
all0.2613 2907 -
obs--99.9 %

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