PDB-8fz9: Crystal Structure of Bacillus cereus TIR protein

ID or keywords:

Entry

Database: PDB / ID: 8fz9

Title

Crystal Structure of Bacillus cereus TIR protein

Components

TIR

Keywords

CHAPERONE / molecular chaperone

Function / homology

CITRIC ACID

Function and homology information

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Khudaverdyan, N. / Song, J.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Toll/interleukin-1 receptor like protein from Bacillus cereus (BcTir)
Authors: Khudaverdyan, N. / Song, J.

History

Deposition	Jan 27, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fz9.cif.gz	128.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8fz9.ent.gz	99 KB	Display	PDB format
PDBx/mmJSON format	8fz9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8fz9_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	8fz9_full_validation.pdf.gz	1 MB	Display
Data in XML	8fz9_validation.xml.gz	16.9 KB	Display
Data in CIF	8fz9_validation.cif.gz	25 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fz/8fz9 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/8fz9	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: TIR

B: TIR

hetero molecules

32 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: TIR

hetero molecules

defined by author&software
Evidence: gel filtration
16 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: TIR

hetero molecules

defined by author&software
16 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	32.695, 38.285, 66.822
Angle α, β, γ (deg.)	102.27, 95.75, 101.91
Int Tables number	1
Space group name H-M	P1
Symmetry operation	#1: x,y,z

#1: Protein	TIR Mass: 15793.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.38 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.03 M Citric Acid, 0.07 M Bis-Tris, pH 7.6, 20% PEG 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.78→64.55 Å / Num. obs: 27618 / % possible obs: 94.2 % / Redundancy: 3 % / CC_1/2: 0.987 / R_merge(I) obs: 0.088 / R_pim(I) all: 0.061 / R_rim(I) all: 0.108 / Net I/σ(I): 9.1 / Num. measured all: 81850
Reflection shell	Resolution: 1.78→1.82 Å / % possible obs: 88.3 % / Redundancy: 2.9 % / R_merge(I) obs: 0.541 / Num. measured all: 4421 / Num. unique obs: 1513 / CC_1/2: 0.76 / R_pim(I) all: 0.378 / R_rim(I) all: 0.663 / Net I/σ(I) obs: 2.3

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.78→36.37 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1944	2000	7.26 %
R_work	0.1613	-	-
obs	0.1637	27533	93.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.78→36.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2096	0	26	374	2496

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	2173
X-RAY DIFFRACTION	f_angle_d	1.283	2951
X-RAY DIFFRACTION	f_dihedral_angle_d	19.177	301
X-RAY DIFFRACTION	f_chiral_restr	0.079	335
X-RAY DIFFRACTION	f_plane_restr	0.012	374

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.78-1.83	0.3218	134	0.2468	1707	X-RAY DIFFRACTION	88
1.83-1.88	0.2237	130	0.2318	1666	X-RAY DIFFRACTION	86
1.88-1.93	0.2587	145	0.1984	1848	X-RAY DIFFRACTION	94
1.93-1.99	0.2399	141	0.1981	1801	X-RAY DIFFRACTION	94
1.99-2.06	0.2452	147	0.1735	1867	X-RAY DIFFRACTION	95
2.06-2.15	0.2083	144	0.1615	1847	X-RAY DIFFRACTION	95
2.15-2.24	0.1896	144	0.1648	1839	X-RAY DIFFRACTION	95
2.24-2.36	0.208	144	0.1617	1832	X-RAY DIFFRACTION	94
2.36-2.51	0.2173	145	0.1692	1856	X-RAY DIFFRACTION	95
2.51-2.7	0.2157	138	0.1726	1762	X-RAY DIFFRACTION	92
2.7-2.98	0.195	149	0.1635	1914	X-RAY DIFFRACTION	97
2.98-3.41	0.1927	147	0.1513	1867	X-RAY DIFFRACTION	98
3.41-4.29	0.1588	146	0.1298	1870	X-RAY DIFFRACTION	96
4.29-36.37	0.1535	146	0.1537	1857	X-RAY DIFFRACTION	96

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.8014	0.104	-0.4247	5.1891	-2.0358	3.7833	-0.0997	-0.1072	-0.2528	0.5109	-0.3066	-0.3908	-0.0518	0.1473	0.3322	0.1802	-0.0233	-0.0051	0.2353	0.0315	0.1973	-0.4516	-4.6256	7.0703
2	2.3867	0.505	-0.6243	2.594	0.5311	2.4468	0.1248	-0.2821	-0.0243	0.1017	-0.0201	-0.3546	-0.0967	0.2209	-0.1318	0.1589	-0.0093	-0.0024	0.2218	0.0096	0.2085	7.608	1.1475	8.6869
3	0.7271	0.6103	0.8055	0.6729	0.2719	2.357	0.0507	0.4065	-0.2044	-0.101	0.0433	0.0388	0.0875	0.1514	-0.0882	0.1981	0.0194	0.0139	0.2629	-0.006	0.1912	-1.8652	-3.2368	-5.4655
4	0.997	0.4227	0.8079	1.7286	-0.8969	5.8899	-0.0004	-0.0069	-0.4666	0.0561	0.1814	-0.2725	0.5884	-0.4246	-0.1439	0.2844	-0.0309	-0.0302	0.2347	-0.0298	0.2471	-6.8618	-9.7225	-3.956
5	1.4727	-0.6663	0.3813	1.8761	-0.7873	2.9613	0.0749	0.0727	-0.0389	-0.0842	-0.008	0.2052	0.0471	-0.2883	-0.044	0.1265	-0.002	-0.0106	0.1844	0.0207	0.1398	-8.4397	-0.0395	2.1128
6	2.0162	0.3381	0.052	2.2345	0.0956	1.7969	0.1853	-0.2192	0.1327	0.2948	-0.1564	0.0282	-0.136	-0.0804	-0.0401	0.1673	-0.0011	0.01	0.1768	0.0109	0.1542	-6.183	6.6541	8.4695
7	3.2357	0.683	-0.3619	2.063	0.8819	1.416	0.1172	-0.0098	0.1318	-0.0271	-0.0631	0.2819	-0.1598	-0.1616	0.0291	0.1718	0.0099	0.0109	0.2369	-0.0009	0.1946	-11.0415	6.0385	9.6565
8	3.7576	0.1434	-0.558	2.4534	-0.2518	1.7689	0.0511	-0.6331	-0.0624	0.3868	-0.0044	-0.1629	0.054	0.0283	-0.0679	0.2113	-0.0482	-0.0162	0.3117	0.0253	0.1497	-0.3255	2.0462	17.7501
9	9.4947	-1.1121	-1.3196	2.0263	-0.0207	8.7398	0.9273	-0.7602	-0.5127	0.2154	0.1557	1.4794	-0.149	-0.7251	0.5539	0.2909	0.0317	-0.0882	0.4051	0.2557	0.5351	-12.0196	-7.4998	20.4483
10	2.6928	-0.9348	-0.5955	1.7077	-0.2899	2.3908	0.0505	-0.1877	0.1563	0.084	0.0233	-0.1225	-0.0269	0.3251	-0.071	0.1385	-0.0011	-0.0063	0.163	-0.026	0.1557	-6.179	17.9354	33.4216
11	1.8695	0.3037	-0.8912	1.8754	0.0463	1.5534	0.0676	-0.4308	-0.2885	0.235	-0.1552	0.0231	0.5412	0.2674	0.0164	0.2986	0.026	-0.0168	0.2071	0.044	0.1941	-16.1697	10.7807	45.0332
12	1.8756	0.1104	-0.1708	2.1839	0.1768	2.4932	-0.0066	0.0095	-0.1112	-0.0159	0.0128	-0.145	0.198	-0.0889	0.046	0.1608	0.0009	-0.0111	0.1436	-0.0167	0.1711	-17.5376	12.3477	32.6487
13	1.062	0.3219	-0.1999	3.9272	0.0711	1.9942	-0.0061	-0.1674	-0.2049	0.3277	-0.0576	0.4776	0.1264	-0.1621	0.0234	0.187	-0.0094	0.0092	0.1849	0.005	0.185	-22.9512	14.3027	40.0939
14	1.8706	-0.2606	-0.8801	1.7479	0.5761	2.767	0.0267	0.2652	-0.0426	-0.1584	-0.1063	0.081	-0.1003	-0.1991	0.0263	0.1568	-0.0081	-0.0026	0.1647	0.0016	0.1749	-17.9375	15.4198	27.6167
15	4.319	-2.7084	-0.0954	4.1541	0.2659	2.427	0.118	0.2953	-0.5268	-0.0273	0.0304	0.5156	0.4903	-0.7567	0.0235	0.1239	-0.0244	-0.0116	0.2777	0.0153	0.1928	-27.8845	12.7665	30.7836
16	2.4122	0.2151	-1.1124	1.087	-0.6491	1.5582	-0.0564	0.1998	0.4468	-0.0783	0.0179	0.0978	0.1498	-0.1808	-0.0249	0.1589	-0.0023	-0.0167	0.2266	0.014	0.1916	-19.3188	19.0942	24.844
17	0.295	0.2283	0.1062	0.4448	-0.1916	0.3753	0.3302	0.0284	0.7348	-0.145	0.0335	0.0521	-0.4717	-0.0857	-0.1338	0.2234	-0.0034	0.0343	0.1847	0.0398	0.2951	-13.5833	27.0538	27.8063

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 10 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 11 through 35 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 47 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 48 through 61 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 62 through 89 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 90 through 106 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 107 through 120 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 121 through 129 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 130 through 136 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 35 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 36 through 61 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 62 through 77 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 78 through 88 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 89 through 106 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 107 through 111 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 112 through 120 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 121 through 132 )

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