PDB-4zhv: Crystal structure of a bacterial signalling protein

ID or keywords:

Entry

Database: PDB / ID: 4zhv

Title

Crystal structure of a bacterial signalling protein

Components

YfiB

Keywords

SIGNALING PROTEIN /

Outer membrane protein /

signalling

Function / homology

Function and homology information

cell outer membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.585 Å

Authors

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

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	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	4zhv.cif.gz	168.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zh/4zhv ftp://data.pdbj.org/pub/pdb/validation_reports/zh/4zhv	HTTPS FTP

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Related structure data

Related structure data	4zhuC 4zhwC 4zhyC C: citing same article (ref.)
Similar structure data	2q3q-d 1rv1-d 4dtl-d 4dtf-d 5k5a-d 1vjh-d 4dtd-d 4e4c-1 3o6b-2 4y13-d 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	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: YfiB

B: YfiB

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	36.841, 56.418, 139.568
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	YfiB Mass: 18433.986 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: yfiB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4L6
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 277 / 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: 1.97 Å³/Da / Density % sol: 37.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 2% PEG 400, 2.0 M ammonium sulfate

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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: Mar 2, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.58→50 Å / Num. obs: 40264 / % possible obs: 99.7 % / Redundancy: 6.4 % / Net I/σ(I): 37.8

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Processing

Software

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

Refinement

Resolution: 1.585→35.893 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1882	2009	5 %
R_work	0.1664	-	-
obs	0.1675	40140	99.23 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.585→35.893 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2107	0	5	277	2389

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2137
X-RAY DIFFRACTION	f_angle_d	1.201	2877
X-RAY DIFFRACTION	f_dihedral_angle_d	14.039	820
X-RAY DIFFRACTION	f_chiral_restr	0.048	314
X-RAY DIFFRACTION	f_plane_restr	0.006	390

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 (%)
1.5854-1.625	0.2668	128	0.2347	2549	X-RAY DIFFRACTION	94
1.625-1.669	0.2207	115	0.2134	2718	X-RAY DIFFRACTION	99
1.669-1.7181	0.2401	137	0.1973	2683	X-RAY DIFFRACTION	100
1.7181-1.7735	0.2241	141	0.1906	2714	X-RAY DIFFRACTION	100
1.7735-1.8369	0.2258	150	0.1827	2683	X-RAY DIFFRACTION	100
1.8369-1.9104	0.1889	156	0.1696	2673	X-RAY DIFFRACTION	100
1.9104-1.9974	0.2028	123	0.1735	2727	X-RAY DIFFRACTION	100
1.9974-2.1027	0.2189	142	0.1654	2737	X-RAY DIFFRACTION	100
2.1027-2.2344	0.171	147	0.1583	2692	X-RAY DIFFRACTION	100
2.2344-2.4069	0.1772	162	0.1525	2733	X-RAY DIFFRACTION	100
2.4069-2.649	0.1798	175	0.1684	2723	X-RAY DIFFRACTION	100
2.649-3.0322	0.2152	143	0.1793	2769	X-RAY DIFFRACTION	100
3.0322-3.8195	0.1712	144	0.1674	2790	X-RAY DIFFRACTION	100
3.8195-35.9025	0.1734	146	0.1503	2940	X-RAY DIFFRACTION	99

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	0.0797	-0.1119	-0.007	0.2246	-0.0038	-0.0021	-0.1664	-0.4129	0.2159	0.0399	0.0757	-0.6734	0.085	0.4781	0.0004	0.3025	-0.1023	0.0312	0.5025	-0.0821	0.3892	53.0656	66.4047	9.818
2	0.0593	0.0517	-0.0299	0.0809	-0.0024	0.0305	-0.1418	0.1439	-0.0325	-0.5529	0.1594	0.0664	0.1035	-0.0485	-0	0.2872	-0.0637	0.0269	0.2446	-0.014	0.2462	40.4879	66.3319	4.5176
3	0.0233	0.0155	0.0144	0.0362	0.0407	0.0145	0.3912	-0.2337	-0.0773	0.4463	-0.2119	0.0429	-0.1098	0.0034	-0.001	0.3077	-0.0896	0.0145	0.2947	-0.0314	0.2836	41.928	66.1369	17.0011
4	0.1185	-0.0067	-0.2283	0.2137	-0.006	0.3849	0.0353	0.0551	0.096	0.0998	0.0679	0.025	-0.1447	-0.0346	-0	0.223	-0.0266	0.0099	0.2391	0.0127	0.2285	29.2549	54.1979	17.381
5	0.1514	0.2233	0.2285	0.1247	0.1853	0.5005	-0.1072	0.0523	-0.0921	-0.2351	0.1411	-0.0484	0.062	-0.1684	0	0.1948	-0.0218	0.0139	0.2327	0.0004	0.2043	32.4507	54.0221	5.4024
6	0.3298	0.083	0.2106	0.6502	-0.1525	0.1942	0.021	-0.1933	-0.1314	0.1615	-0.1171	-0.2058	-0.1635	0.2564	0.0003	0.2702	-0.0479	-0.0011	0.2383	0.0048	0.2143	37.8715	54.7604	20.8618
7	0.3391	0.3262	-0.233	1.0464	0.0321	0.0796	0.0641	-0.1026	-0.2448	0.112	-0.1382	-0.2819	0.1775	0.0371	-0.0002	0.2296	-0.0251	-0.0257	0.2305	0.0241	0.2563	37.9047	48.1097	17.9387
8	0.0973	-0.0213	-0.1234	0.0813	-0.0569	0.1377	0.0837	-0.091	0.476	0.4185	0.0122	-0.2043	-0.6398	-0.0168	-0.0003	0.4937	-0.0287	0.0311	0.3016	-0.0424	0.2597	30.7805	61.5323	29.7686
9	0.1454	0.0873	0.2223	0.0863	0.0939	0.28	0.3361	-0.3443	0.2311	0.1376	-0.0801	-0.1075	0.125	0.1954	0.0005	0.2396	-0.0692	0.0271	0.2885	-0.0334	0.299	40.1832	59.2038	17.3275
10	0.0717	0.0736	0.0878	0.1614	-0.0246	0.1564	-0.1227	0.1204	0.0009	-0.1869	0.1025	-0.0152	-0.0503	0.0346	0.0002	0.2464	-0.0533	-0.0003	0.2297	0.0021	0.2673	10.6746	19.1356	6.7325
11	0.1057	-0.024	0.0601	0.0464	-0.0375	0.0484	0.0801	-0.1859	-0.0833	0.5967	-0.2055	-0.354	0.0521	-0.0534	-0.0003	0.3573	-0.0833	-0.0099	0.2879	0.0168	0.2504	13.3112	20.314	17.6787
12	0.1153	0.2417	0.0478	0.0493	0.016	0.372	0.2009	-0.0207	-0.2952	0.2873	-0.0332	-0.309	0.1137	0.0168	-0.0001	0.2399	-0.0312	-0.0589	0.2313	0.0018	0.2963	25.6924	31.8281	18.5773
13	0.0662	0.1338	0.0294	0.1102	-0.1348	0.3229	0.0027	0.1325	-0.1692	-0.1537	0.1072	-0.0796	0.164	0.2027	0	0.2113	-0.025	-0.0076	0.2389	-0.0113	0.2048	22.2337	30.7157	6.711
14	0.3568	0.2469	-0.2524	0.7081	0.0274	0.203	0.0274	-0.2227	0.0333	0.1978	-0.1832	0.1198	-0.0834	-0.2219	-0.0002	0.2974	-0.0641	-0.0005	0.2732	0.0032	0.2347	16.8864	32.0048	22.3263
15	0.3887	0.2808	0.2344	1.1542	-0.1629	0.1082	0.0825	-0.1042	0.0204	0.07	-0.0568	0.2015	-0.2233	-0.0051	0	0.1846	-0.0269	0.0072	0.2383	-0.0116	0.2324	17.1905	38.3344	18.6159
16	0.679	-0.2674	0.6773	0.4926	-0.4441	0.8067	0.1022	-0.6828	-0.1002	0.6894	-0.1254	-0.0893	0.6868	-0.4761	-0.1852	0.6612	-0.1897	-0.1112	0.4188	0.1505	0.2308	20.5386	26.5156	33.4584
17	0.0108	0.0179	-0.1059	0.2368	0.0072	0.2601	0.2898	0.0759	-0.4931	0.225	-0.0147	0.0284	0.2062	0.1046	0.0008	0.3244	-0.0748	-0.0863	0.2646	0.0276	0.2951	21.6298	26.2716	24.5825

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 46 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 47 through 53 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 54 through 73 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 74 through 90 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 91 through 106 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 107 through 139 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 140 through 158 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 159 through 168 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 34 through 45 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 46 through 53 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 54 through 73 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 74 through 90 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 91 through 106 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 107 through 139 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 140 through 151 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 152 through 167 )

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