PDB-5caj: Crystal structure of E. coli YaaA, a member of the DUF328/UPF0246...

ID or keywords:

Entry

Database: PDB / ID: 5caj

Title

Crystal structure of E. coli YaaA, a member of the DUF328/UPF0246 family

Components

UPF0246 protein YaaA

Keywords

UNKNOWN FUNCTION

Function / homology

Peroxide stress protein YaaA / Peroxide stress protein YaaA / response to hydroperoxide /

cytosol /

BENZAMIDINE / Peroxide stress resistance protein YaaA

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.65 Å

Authors

Prahlad, J. / Lin, J. / Wilson, M.A.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: The DUF328 family member YaaA is a DNA-binding protein with a novel fold.
Authors: Prahlad, J. / Yuan, Y. / Lin, J. / Chang, C.W. / Iwata-Reuyl, D. / Liu, Y. / de Crecy-Lagard, V. / Wilson, M.A.

History

Deposition	Jun 29, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 24, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Jul 8, 2020	Group: Data collection / Category: diffrn_radiation_wavelength / diffrn_source Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.4	Oct 28, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5caj.cif.gz	233.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5caj.ent.gz	195.6 KB	Display	PDB format
PDBx/mmJSON format	5caj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ca/5caj ftp://data.pdbj.org/pub/pdb/validation_reports/ca/5caj	HTTPS FTP

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Related structure data

Similar structure data	5y61-1 4gt4-1 3my0-3 7a21-1 3u0j-1 2xnj-2 6ikk-1 4i3y-2 3owu-2 6t2n-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: UPF0246 protein YaaA

B: UPF0246 protein YaaA

hetero molecules

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

1

A: UPF0246 protein YaaA

hetero molecules

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

2

B: UPF0246 protein YaaA

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.664, 77.060, 184.161
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	UPF0246 protein YaaA Mass: 32121.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yaaA, b0006, JW0005 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A8I3
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-BEN / BENZAMIDINE / Benzamidine Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₈N₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.3 % / Description: prismatic rods
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 15% PEG 8000, 0.1 M dibasic sodium phosphate, 0.075 M monobasic sodium phosphate, 0.1 M sodium citrate 4.6, 0.1 M NaCl, 3% w/v benzamidine HCl Temp details: room temperature

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9788 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9788 Å / Relative weight: 1
Reflection	Resolution: 1.65→50 Å / Num. all: 150892 / Num. obs: 150892 / % possible obs: 99.9 % / Redundancy: 3.1 % / R_sym value: 0.073 / Net I/σ(I): 15.6
Reflection shell	Resolution: 1.65→1.71 Å / Redundancy: 3 % / R_merge(I) obs: 0.779 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.9_1692	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.65→40.91 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / Phase error: 16.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1758	7499	4.97 %	random
R_work	0.151	-	-	-
obs	0.1523	150790	99.86 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→40.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4212	0	13	551	4776

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4413
X-RAY DIFFRACTION	f_angle_d	1.224	5969
X-RAY DIFFRACTION	f_dihedral_angle_d	12.521	1682
X-RAY DIFFRACTION	f_chiral_restr	0.05	641
X-RAY DIFFRACTION	f_plane_restr	0.007	785

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 (%)
1.6504-1.6691	0.2866	228	0.2873	4716	X-RAY DIFFRACTION	98
1.6691-1.6887	0.2879	290	0.2657	4788	X-RAY DIFFRACTION	100
1.6887-1.7093	0.2753	230	0.2533	4782	X-RAY DIFFRACTION	100
1.7093-1.731	0.2626	219	0.2403	4775	X-RAY DIFFRACTION	100
1.731-1.7538	0.2411	278	0.2246	4868	X-RAY DIFFRACTION	100
1.7538-1.7778	0.2189	233	0.2142	4686	X-RAY DIFFRACTION	100
1.7778-1.8032	0.2076	251	0.2048	4791	X-RAY DIFFRACTION	100
1.8032-1.8301	0.2009	248	0.1882	4855	X-RAY DIFFRACTION	100
1.8301-1.8587	0.1968	255	0.1782	4685	X-RAY DIFFRACTION	100
1.8587-1.8892	0.1823	245	0.1757	4818	X-RAY DIFFRACTION	100
1.8892-1.9217	0.2146	245	0.1629	4791	X-RAY DIFFRACTION	100
1.9217-1.9567	0.1684	247	0.1621	4773	X-RAY DIFFRACTION	100
1.9567-1.9943	0.2021	233	0.1622	4828	X-RAY DIFFRACTION	100
1.9943-2.035	0.1832	253	0.1437	4785	X-RAY DIFFRACTION	100
2.035-2.0793	0.1675	247	0.1367	4779	X-RAY DIFFRACTION	100
2.0793-2.1276	0.1604	258	0.136	4729	X-RAY DIFFRACTION	100
2.1276-2.1808	0.1505	260	0.1361	4825	X-RAY DIFFRACTION	100
2.1808-2.2398	0.1719	233	0.1335	4754	X-RAY DIFFRACTION	100
2.2398-2.3057	0.1787	256	0.137	4787	X-RAY DIFFRACTION	100
2.3057-2.3801	0.1573	257	0.1326	4783	X-RAY DIFFRACTION	100
2.3801-2.4652	0.1785	261	0.1346	4748	X-RAY DIFFRACTION	100
2.4652-2.5639	0.1789	238	0.1449	4798	X-RAY DIFFRACTION	100
2.5639-2.6805	0.1646	253	0.1429	4774	X-RAY DIFFRACTION	100
2.6805-2.8218	0.1848	234	0.1424	4786	X-RAY DIFFRACTION	100
2.8218-2.9986	0.161	295	0.1458	4701	X-RAY DIFFRACTION	100
2.9986-3.23	0.1746	241	0.1467	4819	X-RAY DIFFRACTION	100
3.23-3.5549	0.1707	254	0.1466	4771	X-RAY DIFFRACTION	100
3.5549-4.0689	0.1642	259	0.1334	4764	X-RAY DIFFRACTION	100
4.0689-5.1248	0.135	243	0.1176	4781	X-RAY DIFFRACTION	100
5.1248-40.9223	0.1788	255	0.1651	4751	X-RAY DIFFRACTION	100

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	0.1662	-0.1795	-0.2021	0.2795	0.0287	0.2647	-0.0417	-0.0001	-0.0752	0.1063	0.0166	-0.01	-0.0331	0.0916	-0.0001	0.164	-0.0189	0.0193	0.1651	-0.0186	0.1756	-6.821	27.9433	109.8271
2	0.92	-0.1654	0.0683	0.5108	-0.0846	0.3667	-0.0251	0.0444	-0.0075	0.0086	0.0312	0.0187	-0.0198	-0.0175	0	0.1469	-0.0176	0.0107	0.1348	-0.0199	0.1299	-13.3747	33.8523	105.8378
3	0.7259	-0.4499	-0.5602	0.5993	0.2379	0.4851	0.0188	0.2035	-0.1031	-0.1167	-0.0331	-0.0328	0.0141	-0.0035	-0.0002	0.1688	-0.0175	0.0278	0.1672	-0.0205	0.1481	-2.8811	26.0025	97.2264
4	0.1976	-0.1161	0.1453	0.1289	0.087	0.4999	0.011	0.0006	-0.1888	-0.051	0.0162	-0.0747	0.2971	-0.0663	-0.0004	0.2503	-0.0603	0.0217	0.1644	-0.0167	0.2213	-4.7393	10.4757	103.4967
5	0.3444	-0.2182	0.2096	0.5651	-0.1025	0.7216	-0.0442	-0.1683	-0.1049	0.0275	0.0157	-0.0283	0.2114	-0.0698	-0.0035	0.2455	-0.0194	0.0216	0.162	0.0229	0.1868	-4.1555	10.5228	113.5897
6	0.1132	-0.1799	0.0915	0.1781	-0.0938	0.2708	-0.0428	-0.1182	0.1122	0.0336	0.0799	0.0349	0.1156	-0.0442	-0	0.1638	-0.0021	0.0069	0.1861	-0.015	0.1907	13.824	53.3579	122.7077
7	0.3479	-0.2373	-0.0847	0.4182	0.3263	0.2465	-0.0024	0.1464	-0.0329	-0.1424	-0.054	0.1137	0.1326	0.0013	-0.0001	0.1797	-0.0175	0.0082	0.1964	0.0036	0.1807	17.3859	52.0346	109.5521
8	0.4524	-0.2396	0.2099	0.2523	0.1601	0.546	-0.0831	0.1032	0.1529	-0.0583	0.0685	-0.0257	0.029	0.062	-0.0002	0.1348	-0.0145	0.023	0.1376	-0.0034	0.2024	28.9926	56.3671	110.0577
9	0.5778	-0.4198	-0.265	0.3179	0.1728	0.3962	-0.0619	-0.0157	-0.0286	0.0344	0.0481	0.0396	0.001	0.0356	0.0749	0.1525	-0.0084	0.0174	0.146	-0.0068	0.172	15.8197	50.9411	122.3028
10	0.1208	-0.0822	-0.0378	0.0845	-0.0017	0.0572	0.0169	0.1839	0.5154	-0.0216	-0.0952	-0.1535	-0.1572	0.2803	0.0098	0.2157	-0.0068	0.018	0.2217	0.0877	0.2848	19.4934	69.347	109.2521
11	0.2899	-0.2484	0.0729	0.2576	0.0353	0.2551	-0.0302	-0.0561	0.1148	0.0035	0.0158	0.0597	-0.1075	-0.1409	0	0.16	0.0082	0.0038	0.2199	-0.0094	0.2078	6.3298	63.112	118.9043
12	0.5343	-0.2705	-0.4724	0.4391	-0.1365	0.733	-0.0365	-0.2648	0.0734	0.1364	0.0551	0.1233	-0.0385	0.044	0.0155	0.2148	0.0097	0.023	0.24	-0.051	0.1856	13.6278	63.8209	133.7159
13	0.2701	-0.1129	-0.4418	0.2715	0.3024	0.6193	-0.0475	-0.2183	-0.0578	0.1234	0.0275	0.0994	-0.0334	0.0003	0.0021	0.2754	0.0589	0.04	0.2927	-0.0106	0.1905	8.8292	61.9426	140.9241

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -4 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 129 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 130 through 178 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 179 through 204 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 205 through 256 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid -4 through 15 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 16 through 40 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 41 through 78 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 79 through 129 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 130 through 142 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 143 through 178 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 179 through 221 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 222 through 256 )

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