PDB-6ikj: Crystal structure of YfiB(F48S)

ID or keywords:

Entry

Database: PDB / ID: 6ikj

Title

Crystal structure of YfiB(F48S)

Components

YfiB

Keywords

SIGNALING PROTEIN / signalling system /

peptidoglycan binding

Function / homology

Function and homology information

cell outer membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Li, S. / Zhang, Q. / Bartlam, M.

Funding support

China, 1items

Citation

Journal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural analysis of activating mutants of YfiB from Pseudomonas aeruginosa PAO1.
Authors: Li, S. / Li, T. / Teng, X. / Lou, X. / Xu, Y. / Zhang, Q. / Bartlam, M.

History

Deposition	Oct 16, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ikj.cif.gz	170.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ik/6ikj ftp://data.pdbj.org/pub/pdb/validation_reports/ik/6ikj	HTTPS FTP

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Related structure data

Related structure data	6ikiC 6ikkC 4zhwS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3k42-2 2o6p-d 3lra-d 3g9h-d 6v0s-1 4eiz-2 4ej1-2 3c0v-5 3u2h-d 3noi-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

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

1

Idetical with deposited unit
defined by author
Evidence: equilibrium centrifugation

Unit cell

Length a, b, c (Å)	37.206, 56.300, 139.896
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: 18373.891 Da / Num. of mol.: 2 / Mutation: F48S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: yfiB, PA1119 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.0M (NH4)2SO4, 0.1M CAPS pH 10.5, 0.2 M Li2SO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.76→37.21 Å / Num. obs: 29728 / % possible obs: 98.9 % / Redundancy: 6.1 % / R_merge(I) obs: 0.091 / Net I/σ(I): 32.2
Reflection shell	Resolution: 1.76→1.79 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.448 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1335 / % possible all: 92.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ZHW

4zhw

Resolution: 1.76→35.956 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.82

	R_factor	Num. reflection	% reflection
R_free	0.2302	1994	6.74 %
R_work	0.1919	-	-
obs	0.1945	29598	98.67 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.76→35.956 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2067	0	11	188	2266

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2098
X-RAY DIFFRACTION	f_angle_d	0.992	2821
X-RAY DIFFRACTION	f_dihedral_angle_d	16.957	1296
X-RAY DIFFRACTION	f_chiral_restr	0.058	309
X-RAY DIFFRACTION	f_plane_restr	0.007	382

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 (%)
1.7604-1.8044	0.3322	129	0.2636	1805	X-RAY DIFFRACTION	94
1.8044-1.8532	0.3008	139	0.2585	1911	X-RAY DIFFRACTION	97
1.8532-1.9077	0.3642	138	0.2549	1930	X-RAY DIFFRACTION	98
1.9077-1.9693	0.3537	140	0.2784	1929	X-RAY DIFFRACTION	98
1.9693-2.0397	0.2645	142	0.2244	1957	X-RAY DIFFRACTION	99
2.0397-2.1213	0.2716	141	0.2027	1956	X-RAY DIFFRACTION	100
2.1213-2.2179	0.2424	143	0.1949	1967	X-RAY DIFFRACTION	100
2.2179-2.3348	0.2688	144	0.216	1992	X-RAY DIFFRACTION	99
2.3348-2.481	0.2033	141	0.1893	1964	X-RAY DIFFRACTION	99
2.481-2.6725	0.2569	146	0.1965	1999	X-RAY DIFFRACTION	100
2.6725-2.9413	0.2349	143	0.1998	1991	X-RAY DIFFRACTION	100
2.9413-3.3667	0.2159	147	0.1959	2023	X-RAY DIFFRACTION	99
3.3667-4.2406	0.2051	146	0.1639	2034	X-RAY DIFFRACTION	99
4.2406-35.9636	0.1983	155	0.1736	2146	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	2.6613	0.3793	0.9292	2.4333	-1.484	9.6384	0.3124	-0.3871	-0.3653	0.1138	-0.1923	0.1543	0.3748	-0.2804	-0.1646	0.2448	-0.0789	-0.0043	0.2404	0.0306	0.3332	-6.4212	-64.8737	151.6722
2	3.8537	5.4994	-0.0419	7.3223	-0.2189	1.0179	0.1974	0.3286	-0.4573	0.2595	-0.0072	-0.289	0.1825	0.1628	-0.2984	0.2976	-0.0237	-0.0708	0.2377	-0.0357	0.2792	7.4881	-52.8389	158.2998
3	3.7972	5.1314	1.5926	6.672	2.0858	3.1995	-0.0602	0.6417	-0.2755	-0.1801	0.1927	-0.1336	-0.1999	0.5049	-0.168	0.2935	-0.0161	-0.0185	0.2844	-0.0239	0.2289	3.8996	-53.646	146.4668
4	4.0023	3.2124	0.5381	8.1328	5.218	4.1588	-0.0332	-0.3795	0.0741	0.3971	-0.1899	0.1077	0.0199	0.0156	-0.0225	0.2743	-0.0265	0.0715	0.1885	0.0456	0.2078	-1.4022	-52.9201	162.0905
5	3.1074	-0.0224	2.1795	4.5645	1.0539	4.4463	0.1118	-0.1964	0.0173	0.1547	-0.0483	0.1976	-0.521	-0.2524	-0.0001	0.2363	-0.016	0.0185	0.2205	-0.0017	0.2454	-1.1188	-46.2718	158.4231
6	8.5251	-3.7778	2.1178	3.4425	-1.3051	8.6826	-0.3879	-0.2817	-0.5681	1.3571	0.3849	-0.7679	1.1693	0.0489	-0.131	0.6589	-0.0103	-0.1144	0.2681	0.0483	0.4977	5.4502	-58.9033	171.7851
7	5.9563	4.2962	5.6857	2.9936	4.0057	5.1962	0.4609	-0.3773	-0.3698	0.2677	-0.0997	-0.0239	0.0415	-0.1616	-0.1984	0.354	-0.0678	-0.03	0.2806	0.0948	0.329	-3.4412	-57.1768	159.0293
8	2.4566	-1.7708	1.7404	2.2717	-0.2041	2.4265	-0.2495	-0.532	0.0067	0.2696	0.1204	0.5199	0.0558	-0.1702	0.1045	0.2753	0.0451	-0.0125	0.2885	-0.0357	0.4334	5.3696	-65.9821	134.598
9	4.8134	-5.3713	3.9729	8.2841	-3.9197	3.4481	0.4705	0.1431	-0.3242	-0.4882	-0.2056	0.0639	0.5095	0.0352	-0.3424	0.3654	0.0499	-0.0058	0.2279	-0.0082	0.2542	-4.2847	-57.0631	122.336
10	5.6577	-4.6897	4.7823	4.5522	-4.1242	4.06	0.0496	-0.1753	-0.2892	0.407	0.041	-0.0215	0.1215	-0.1142	-0.0882	0.3087	0.0095	-0.0213	0.3074	-0.0199	0.2676	-4.3237	-53.8948	134.3197
11	9.3804	-3.0798	5.2388	4.7662	-4.3655	4.6471	0.2802	0.5973	0.292	-0.3467	-0.5172	-0.3349	0.4351	0.7809	0.2827	0.3025	0.0677	-0.0253	0.2515	-0.0383	0.351	5.9083	-55.1983	125.9141
12	4.6079	0.6656	4.2666	5.251	0.2432	3.7839	0.1419	0.6495	0.2459	-0.6935	-0.0633	-0.1408	-0.0999	0.4925	0.0981	0.2801	0.1033	0.0639	0.3189	0.0324	0.2865	-3.0963	-48.5675	116.8927
13	8.4582	1.3555	7.961	7.8085	1.2075	7.9525	0.1607	0.6455	0.7082	-0.2473	-0.5856	-0.9631	0.0438	1.4048	0.2144	0.2488	0.02	0.0359	0.2964	0.0706	0.3859	7.5123	-49.1494	126.4333
14	5.8748	5.5349	2.6017	5.4086	1.4516	6.283	0.5194	1.0353	-0.5279	-0.5699	0.2704	-0.1709	0.7664	0.1277	-0.6629	0.6649	0.1425	-0.0908	0.3468	-0.0892	0.3835	-6.4671	-61.1914	109.8144
15	9.7604	-5.2426	5.5822	8.0345	-3.5963	3.5517	0.4252	0.6264	-0.5068	0.1967	0.0954	0.142	-0.3295	0.3278	-0.4305	0.463	0.1097	-0.0463	0.3599	-0.0631	0.2996	1.2443	-58.4252	121.7372

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 34 through 53 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 54 through 73 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 74 through 90 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 91 through 106 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 107 through 139 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 140 through 158 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 159 through 168 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 34 through 46 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 47 through 73 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 74 through 90 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 91 through 100 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 101 through 128 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 129 through 139 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 140 through 158 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 159 through 167 )

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