PDB-4zhu: Crystal structure of a bacterial repressor protein

ID or keywords:

Entry

Database: PDB / ID: 4zhu

Title

Crystal structure of a bacterial repressor protein

Components

YfiR

Keywords

TRANSCRIPTION / Periplasmic binding protein / repressor

Function / homology

YfiR/HmsC-like / YfiR/HmsC-like / periplasmic space / Negative regulator YfiR

Function and homology information

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.3968 Å

Authors

Li, S. / Li, T. / Wang, Y. / Bartlam, M.

Funding support

China, 4items

Organization	Grant number	Country
Ministry of Science & Technology	2014CB560709	China
National Science Foundation of China	31450110071	China
National Science Foundation of China	31322012	China
Tianjin Municipal Science and Technology Commission	13JCYBJC20800	China

Citation

Journal: Sci Rep / Year: 2015
Title: Structural insights into YfiR sequestering by YfiB in Pseudomonas aeruginosa PAO1
Authors: Li, S. / Li, T. / Xu, Y. / Zhang, Q. / Zhang, W. / Che, S. / Liu, R. / Wang, Y. / Bartlam, M.

History

Deposition	Apr 27, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4zhu.cif.gz	133.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4zhu.ent.gz	105.6 KB	Display	PDB format
PDBx/mmJSON format	4zhu.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4zhu_validation.pdf.gz	450.5 KB	Display	wwPDB validaton report
Full document	4zhu_full_validation.pdf.gz	453.3 KB	Display
Data in XML	4zhu_validation.xml.gz	14.2 KB	Display
Data in CIF	4zhu_validation.cif.gz	19.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zh/4zhu ftp://data.pdbj.org/pub/pdb/validation_reports/zh/4zhu	HTTPS FTP

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Related structure data

Related structure data	4zhvC 4zhwC 4zhyC C: citing same article (ref.)
Similar structure data	2mu1-d 3lo0-d 3ebk-1 5hae-d 1t2o-3 1tp9-3 1n05-d 1t2p-1 1t2w-1 5dlo-d 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

Deposited unit

A: YfiR

B: YfiR

hetero molecules

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

1

A: YfiR

hetero molecules

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

2

B: YfiR

hetero molecules

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

Unit cell

Length a, b, c (Å)	121.268, 121.268, 85.482
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-332- HOH
2	1	B-337- HOH

#1: Protein	YfiR Mass: 20704.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: yfiR / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4L4
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.79 Å³/Da / Density % sol: 67.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 1.5M lithium sulfate monohydrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3968→50 Å / Num. obs: 25665 / % possible obs: 99.1 % / Redundancy: 6.5 % / Net I/σ(I): 20.2

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASES		phasing

Refinement

Resolution: 2.3968→36.543 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2113	1004	4.74 %
R_work	0.1814	-	-
obs	0.1829	21162	82.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3968→36.543 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2290	0	15	109	2414

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2339
X-RAY DIFFRACTION	f_angle_d	1.16	3169
X-RAY DIFFRACTION	f_dihedral_angle_d	14.987	873
X-RAY DIFFRACTION	f_chiral_restr	0.045	363
X-RAY DIFFRACTION	f_plane_restr	0.005	416

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 (%)
2.3968-2.5231	0.2268	101	0.1998	1794	X-RAY DIFFRACTION	53
2.5231-2.6811	0.2438	106	0.2045	2083	X-RAY DIFFRACTION	61
2.6811-2.8881	0.2852	134	0.2119	2540	X-RAY DIFFRACTION	74
2.8881-3.1786	0.2509	131	0.2175	3086	X-RAY DIFFRACTION	89
3.1786-3.6381	0.2311	166	0.1814	3465	X-RAY DIFFRACTION	100
3.6381-4.5823	0.1736	172	0.1528	3514	X-RAY DIFFRACTION	100
4.5823-36.5471	0.194	194	0.1789	3676	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	6.2228	-2.4016	1.4896	5.1465	-1.2567	3.2917	0.182	0.214	-0.8432	0.286	-0.2565	0.7232	0.1444	0.1156	-0.0968	0.2006	-0.0109	0.0597	0.2052	0.0068	0.2645	91.912	35.0349	26.6029
2	1.5519	1.9493	0.9179	3.9792	-0.7174	2.7576	-0.434	0.5119	1.1736	-0.8468	0.0561	1.4587	-0.7617	-0.8979	-0.363	0.5729	0.0486	-0.1704	0.1786	0.209	0.4619	87.6859	52.4225	15.8184
3	2.4376	-0.496	-0.3198	1.7595	0.302	1.1907	0.0562	0.2125	0.2091	-0.1902	-0.0373	-0.0587	-0.1515	0.0777	-0.0587	0.2644	-0.0069	0.0148	0.2339	0.0772	0.2059	99.776	42.8445	18.7256
4	7.1839	-2.2721	3.538	3.2989	-1.2233	5.0501	-0.4937	-0.5583	2.2038	-0.1672	-0.1077	-0.8022	-0.7663	1.0008	0.1551	0.3641	-0.0864	-0.0314	0.4634	-0.1021	0.4642	108.6618	53.7982	26.9217
5	1.5782	0.0495	-0.9534	3.3468	-0.0184	0.5517	0.1232	-0.201	0.1927	0.201	-0.1371	0.0736	-0.2698	0.2411	0.0791	0.3943	-0.0203	-0.0544	0.2482	0.0161	0.1753	98.8746	48.8064	26.6352
6	1.9241	0.4106	-0.0674	3.5543	-0.0925	1.5342	-0.2101	-0.5589	0.4647	0.26	0.2347	-0.7789	-0.3267	0.0368	-0.165	0.3617	0.0169	0.0258	0.2864	-0.0756	0.2576	97.7107	46.2108	33.1921
7	2.5656	-1.5094	-0.3474	4.0516	-3.9164	5.3389	0.4111	-0.2853	0.2466	1.1585	-0.5287	0.2377	0.3312	-0.3899	0.1141	0.4694	0.0168	0.0615	0.2686	-0.0296	0.2413	91.4833	38.3934	35.6789
8	2.6959	2.3144	-1.3411	2.9723	-0.1911	2.9277	0.0331	0.0776	0.8705	0.0783	0.0212	0.6083	-0.8127	-0.1985	-0.0888	0.3485	0.0403	0.0754	0.1721	-0.0172	0.4456	90.7308	55.9299	28.3154
9	2.0876	0.9668	0.4496	3.866	-2.1385	2.668	-0.5677	-0.836	0.3196	0.8867	1.1024	0.9811	0.1261	-0.7747	-0.1997	0.4373	0.0254	0.1773	0.4783	-0.0228	0.349	83.1759	41.8878	34.8348
10	4.8489	1.4257	-0.1331	3.9716	-0.598	2.3547	-0.1861	0.4375	-0.3619	-0.7298	0.0586	-0.1167	0.1862	0.1067	0.0392	0.3978	-0.0217	0.0725	0.255	-0.1192	0.277	91.9275	64.2366	36.3679
11	2.7257	-0.4233	0.4827	1.7034	0.0016	1.2328	-0.1046	-0.1566	-0.4367	-0.0799	-0.1076	0.5442	0.16	-0.2122	0.1387	0.3301	-0.0859	0.0902	0.2853	-0.0734	0.4236	83.4352	67.9473	43.4845
12	2.5877	-0.3055	-0.9952	3.6885	0.1578	1.7901	0.038	-0.5338	-0.1271	0.5921	-0.1559	0.7031	0.3261	-0.2818	0.1117	0.4073	-0.0991	0.1607	0.3367	-0.0501	0.3692	84.2442	68.4753	50.9295
13	3.1493	3.3844	-2.1111	5.7739	-3.5872	2.6109	-0.0759	-1.414	-0.7036	1.5813	-0.5883	-1.1058	0.5533	0.6702	0.128	0.7896	0.0918	0.0614	0.5083	-0.0022	0.5893	94.2495	59.8917	52.1481
14	5.1833	1.6987	-2.8214	2.4271	-0.9763	5.249	-0.2181	-0.5925	-0.5622	0.2691	0.0359	-0.2142	0.3463	1.0889	-0.327	0.3948	0.0341	0.0787	0.2069	-0.0874	0.3774	97.505	58.9176	41.1989
15	3.7678	0.6917	-1.5037	0.9376	-0.5128	3.3479	0.2355	-0.715	-0.7948	0.8101	-0.3456	0.1368	0.5741	-0.2432	0.0274	0.7211	-0.1537	0.2257	0.3628	0.0215	0.5268	84.8323	53.4802	49.7161
16	1.315	1.6651	-0.8742	2.975	-3.3875	6.9144	-0.4732	0.1884	-0.7925	0.7251	-0.4752	-0.1919	0.3807	0.8015	-0.2529	0.6922	-0.0586	0.2268	0.1954	-0.1752	0.5347	89.2414	49.2437	41.3735

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 39 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 66 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 67 through 119 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 120 through 130 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 131 through 143 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 144 through 156 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 157 through 164 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 165 through 177 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 178 through 189 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 39 through 58 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 59 through 84 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 85 through 139 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 140 through 150 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 151 through 160 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 161 through 177 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 178 through 185 )

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