PDB-5xi8: Structure and function of the TPR domain

ID or keywords:

Entry

Database: PDB / ID: 5xi8

Title

Structure and function of the TPR domain

Components

Beta-barrel assembly-enhancing protease

Keywords

HYDROLASE / membrane protein / TPR domain

Function / homology

Function and homology information

Gram-negative-bacterium-type cell outer membrane assembly / Hydrolases; Acting on peptide bonds (peptidases) / protein disulfide isomerase activity / chaperone-mediated protein folding / proteolysis involved in protein catabolic process / metalloendopeptidase activity / outer membrane-bounded periplasmic space / zinc ion binding / membrane / metal ion binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.7 Å

Authors

Tanaka, Y. / Tsukazaki, T.

Funding support

Japan, 2items

Citation

Journal: Mol. Microbiol. / Year: 2017
Title: The TPR domain of BepA is required for productive interaction with substrate proteins and the beta-barrel assembly machinery complex.
Authors: Daimon, Y. / Iwama-Masui, C. / Tanaka, Y. / Shiota, T. / Suzuki, T. / Miyazaki, R. / Sakurada, H. / Lithgow, T. / Dohmae, N. / Mori, H. / Tsukazaki, T. / Narita, S.I. / Akiyama, Y.

History

Deposition	Apr 26, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2017	Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2	Dec 13, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5xi8.cif.gz	85.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5xi8_validation.pdf.gz	420.2 KB	Display	wwPDB validaton report
Full document	5xi8_full_validation.pdf.gz	421.3 KB	Display
Data in XML	5xi8_validation.xml.gz	10.4 KB	Display
Data in CIF	5xi8_validation.cif.gz	14.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xi/5xi8 ftp://data.pdbj.org/pub/pdb/validation_reports/xi/5xi8	HTTPS FTP

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Related structure data

Similar structure data	4hop-3 4kd5-4 4hop-1 4hop-2 4cw9-d 5zgm-d 4pob-d 3us4-2 3n4z-d 4ccg-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-barrel assembly-enhancing protease

19.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	103.963, 103.963, 81.491
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-507- HOH
2	1	A-550- HOH
3	1	A-603- HOH
4	1	A-641- HOH
5	1	A-648- HOH
6	1	A-659- HOH
7	1	A-663- HOH
8	1	A-670- HOH

#1: Protein	Beta-barrel assembly-enhancing protease Mass: 19463.230 Da / Num. of mol.: 1 / Fragment: UNP residues 310-482 / Mutation: L450(MSE) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: bepA, yfgC, b2494, JW2479 / Plasmid: pET28 / Production host: Escherichia coli KRX (bacteria) / Strain (production host): KRX References: UniProt: P66948, Hydrolases; Acting on peptide bonds (peptidases)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.18 Å³/Da / Density % sol: 43.51 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS Mosaicity: 0.579 °
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 32% PEG 4000, ammonium acetate, KH2PO4, 2% PEG 8000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-1A / Wavelength: 0.9787, 0.9794, 0.9900

Detector

Type: DECTRIS EIGER X 4M / Detector: CCD / Date: Dec 15, 2015

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9787	1
2	0.9794	1
3	0.99	1

Reflection

Resolution: 1.7→50 Å / Num. obs: 36176 / % possible obs: 100 % / Redundancy: 38.1 % / B_iso Wilson estimate: 18.32 Å² / R_merge(I) obs: 0.272 / R_pim(I) all: 0.047 / R_rim(I) all: 0.277 / Χ²: 1.33 / Net I/σ(I): 4.3 / Num. measured all: 716414

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.7-1.73	20.7	1.001	942	0.816	0.219	1.025	0.384	100
1.73-1.76	29	0.993	919	0.895	0.188	1.01	13.912	100
1.76-1.79	34.5	0.896	933	0.922	0.156	0.91	0.418	100
1.79-1.83	38.7	0.894	935	0.95	0.142	0.905	0.612	100
1.83-1.87	40.7	0.617	912	0.981	0.097	0.625	0.404	100
1.87-1.91	41.3	0.564	937	0.981	0.089	0.571	0.439	100
1.91-1.96	41.6	0.469	931	0.984	0.073	0.475	0.47	100
1.96-2.02	41.9	0.363	935	0.99	0.057	0.368	0.413	100
2.02-2.07	41.4	0.337	937	0.993	0.053	0.341	0.472	100
2.07-2.14	41.3	0.27	932	0.995	0.042	0.274	0.522	100
2.14-2.22	41.1	0.207	931	0.996	0.033	0.209	0.511	100
2.22-2.31	40.1	0.187	935	0.995	0.03	0.189	0.628	100
2.31-2.41	39.6	0.15	940	0.998	0.024	0.151	0.613	100
2.41-2.54	37.9	0.138	963	0.997	0.023	0.14	0.699	100
2.54-2.7	34.4	0.801	922	0.998	0.145	0.815	1.098	100
2.7-2.91	38.5	0.103	944	0.998	0.017	0.105	0.833	100
2.91-3.2	36.8	0.083	937	0.999	0.014	0.084	0.966	100
3.2-3.66	41	0.07	969	0.999	0.011	0.071	1.233	100
3.66-4.61	42.3	0.061	945	0.999	0.01	0.062	1.563	100
4.61-50	38.8	0.066	1007	0.998	0.011	0.067	3.473	99.9

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
PHENIX	1.11_2567	refinement
SCALEPACK		data scaling
SHELX		phasing
PDB_EXTRACT	3.22	data extraction
SHELXD		phasing
HKL-2000		data collection
SHELXE		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.7→37.121 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 17.99 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS

	R_factor	Num. reflection	% reflection
R_free	0.194	3629	10.03 %
R_work	0.1632	32547	-
obs	0.1663	36176	99.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 75.5 Å² / B_iso mean: 22.6603 Å² / B_iso min: 4.73 Å²

Refinement step

Cycle: final / Resolution: 1.7→37.121 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1362	0	0	177	1539
B_iso mean	-	-	-	31.37	-
Num. residues	-	-	-	-	175

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1394
X-RAY DIFFRACTION	f_angle_d	0.979	1886
X-RAY DIFFRACTION	f_chiral_restr	0.042	203
X-RAY DIFFRACTION	f_plane_restr	0.004	260
X-RAY DIFFRACTION	f_dihedral_angle_d	5.902	1188

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.7-1.7224	0.3061	141	0.3011	1251	1392
1.7224-1.746	0.2738	137	0.2458	1264	1401
1.746-1.7709	0.2855	145	0.2456	1265	1410
1.7709-1.7974	0.2844	137	0.2098	1232	1369
1.7974-1.8254	0.2503	137	0.1975	1248	1385
1.8254-1.8554	0.2335	140	0.1895	1247	1387
1.8554-1.8874	0.2359	143	0.1897	1287	1430
1.8874-1.9217	0.2391	139	0.201	1232	1371
1.9217-1.9586	0.1908	134	0.1713	1225	1359
1.9586-1.9986	0.189	144	0.1659	1276	1420
1.9986-2.0421	0.1912	135	0.165	1227	1362
2.0421-2.0896	0.1896	142	0.1635	1259	1401
2.0896-2.1418	0.1516	138	0.1472	1261	1399
2.1418-2.1997	0.1704	142	0.1335	1266	1408
2.1997-2.2644	0.1852	138	0.1509	1239	1377
2.2644-2.3375	0.174	137	0.1355	1252	1389
2.3375-2.421	0.1973	138	0.1529	1247	1385
2.421-2.518	0.1767	141	0.1677	1260	1401
2.518-2.6325	0.2174	139	0.1661	1262	1401
2.6325-2.7713	0.2067	141	0.1529	1214	1355
2.7713-2.9448	0.2284	136	0.1643	1270	1406
2.9448-3.1721	0.2346	140	0.1653	1253	1393
3.1721-3.4911	0.1767	141	0.1472	1262	1403
3.4911-3.9958	0.1723	139	0.1435	1245	1384
3.9958-5.0323	0.1644	140	0.149	1249	1389
5.0323-37.13	0.1533	145	0.1735	1254	1399

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	0.0202	0.0004	0.0044	0.0121	-0.0147	0.0198	-0.1822	-0.226	0.2203	0.01	-0.0816	-0.0786	0.1225	-0.2377	-0	0.0992	-0.0413	0.034	0.1661	0.0377	0.0292	-14.1838	-17.3019	-7.8344
2	0.0134	0.0041	-0.0238	0.0024	0.0039	-0.0004	0.0092	0.0802	0.0749	-0.0659	-0.1207	0.0048	0.0212	-0.0415	0	0.1246	0.0133	0.0022	0.1057	0.0143	0.091	-5.1674	-22.8127	-12.9983
3	0.0036	0.0014	0.0014	0.0017	0.0024	0.0038	-0.0353	0.0099	0.0313	0.0223	-0.0219	0.0052	-0.0275	0.0154	-0	0.1692	-0.0279	-0.083	-0.0616	0.0834	0.4184	7.5352	-22.0124	-9.2667
4	0.0198	0.0237	0.0111	0.0443	-0.0436	0.0269	-0.0142	0.023	-0.0083	0.0252	-0.026	-0.0515	-0.021	-0.0126	0	0.1004	0.005	-0.0028	0.0545	0.0089	0.0738	1.5832	-36.6959	-8.0354
5	-0.0057	0.0021	-0.002	0.0037	0.0133	0.0138	0.0155	-0.0335	-0.0494	-0.0243	-0.0458	0.0015	-0.0931	0.0354	-0	0.0551	-0.0011	-0.0092	0.0395	0.0066	0.0541	2.814	-51.5843	-0.0645
6	0.0138	-0.0189	-0.006	0.0245	0.0011	0.0027	-0.0708	-0.1216	-0.0172	-0.1118	0.1765	-0.0808	-0.134	-0.0246	-0	0.0383	-0.0048	-0.0361	0.0797	-0.0012	0.1011	8.4144	-50.103	8.369

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 308 through 338 )	A	308 - 338
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 339 through 368 )	A	339 - 368
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 369 through 375 )	A	369 - 375
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 376 through 425 )	A	376 - 425
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 426 through 461 )	A	426 - 461
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 462 through 482 )	A	462 - 482

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