PDB-6iki: Crystal structure of YfiB(W55L)

ID or keywords:

Entry

Database: PDB / ID: 6iki

Title

Crystal structure of YfiB(W55L)

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: 2.204 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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Validation report

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

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Related structure data

Related structure data	6ikjC 6ikkC 4zhwS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4xlg-d 7c03-d 3icl-d 3i5q-2 4nkg-1 4az8-d 4nkg-2 3da6-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&software
Evidence: equilibrium centrifugation

Unit cell

Length a, b, c (Å)	44.563, 44.563, 154.934
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	YfiB Mass: 18360.934 Da / Num. of mol.: 2 / Mutation: W55L 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.09 Å³/Da / Density % sol: 41.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30% (w/v) PEG-400, 0.1M cacodylate pH 6.5, 0.2M Li2SO4, 7.5%(w/v) glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9791 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 30, 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: 2.2→44.56 Å / Num. obs: 15242 / % possible obs: 100 % / Redundancy: 13 % / R_merge(I) obs: 0.07 / Net I/σ(I): 36.8
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 9 % / R_merge(I) obs: 0.452 / Mean I/σ(I) obs: 3 / Num. unique obs: 764 / % possible all: 100

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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: 2.204→44.56 Å / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 31.27

	R_factor	Num. reflection	% reflection
R_free	0.2494	1533	10.09 %
R_work	0.2023	-	-
obs	0.2067	15192	99.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.204→44.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2070	0	11	65	2146

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2099
X-RAY DIFFRACTION	f_angle_d	0.983	2820
X-RAY DIFFRACTION	f_dihedral_angle_d	15.45	1303
X-RAY DIFFRACTION	f_chiral_restr	0.053	312
X-RAY DIFFRACTION	f_plane_restr	0.005	383

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 (%)
2.2052-2.2764	0.3387	137	0.3046	1224	X-RAY DIFFRACTION	90
2.2764-2.3577	0.336	137	0.292	1259	X-RAY DIFFRACTION	90
2.3577-2.4521	0.3252	137	0.2857	1217	X-RAY DIFFRACTION	90
2.4521-2.5637	0.2996	136	0.2708	1239	X-RAY DIFFRACTION	90
2.5637-2.6989	0.324	138	0.2817	1245	X-RAY DIFFRACTION	90
2.6989-2.8679	0.3443	139	0.26	1243	X-RAY DIFFRACTION	90
2.8679-3.0893	0.302	146	0.2473	1222	X-RAY DIFFRACTION	89
3.0893-3.4001	0.2703	134	0.2218	1262	X-RAY DIFFRACTION	90
3.4001-3.8919	0.2423	143	0.1838	1219	X-RAY DIFFRACTION	90
3.8919-4.9023	0.1776	141	0.1532	1259	X-RAY DIFFRACTION	90
4.9023-44.5721	0.2209	145	0.1556	1253	X-RAY DIFFRACTION	90

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	2.9148	-0.801	0.2499	0.6212	-0.1668	0.0507	0.0249	0.0253	0.3436	0.7081	0.224	-0.1534	-1.499	0.6833	-0.5371	1.2658	-0.254	0.2039	0.5	-0.0524	-0.0876	5.4125	17.2578	3.9469
2	0.0926	0.2287	0.3178	0.5955	0.4819	1.5144	-0.0069	0.1656	0.0877	0.0906	0.0884	0.2529	-0.5073	-0.2385	0.0008	0.4778	0.0727	0.047	0.4006	0.0026	0.3011	-7.0927	5.7061	14.6434
3	1.0358	0.0572	0.2409	0.1366	0.3348	1.1996	0.4112	0.9462	0.3359	-0.2235	0.1133	0.5068	-0.7658	-1.0645	0.0202	0.4221	0.0725	-0.0163	0.5097	0.0874	0.385	-6.6984	8.0167	2.1074
4	1.2245	-0.1277	0.8757	1.5657	0.2713	0.8438	0.0328	-0.009	-0.1375	0.0295	-0.0428	-0.0969	-0.0433	0.7833	0.0022	0.3253	-0.0281	-0.0181	0.3929	0.0002	0.2811	3.4989	4.1315	15.1544
5	1.6753	0.62	-0.8256	0.9257	0.1796	0.7382	-0.0337	0.1187	-0.17	0.1292	-0.0549	-0.0746	0.1925	-0.0036	-0.0065	0.3781	0.0415	0.0093	0.3148	0.0065	0.3175	-1.2752	-2.179	13.973
6	1.1011	-0.1672	0.5224	1.3337	-1.7468	2.5153	0.2665	-0.0227	0.0333	0.1679	-0.0298	-0.0246	-0.9616	0.7566	0.0087	0.5108	-0.024	0.0305	0.3879	-0.0385	0.2528	2.9023	6.7197	17.347
7	2.6912	0.8611	-0.0643	0.7396	0.0907	0.15	-0.3695	0.4948	-0.4167	0.017	0.7257	0.2053	0.348	-0.6328	-0.0447	0.6812	0.0478	-0.4338	0.5438	0.1623	1.1859	-32.7664	-18.8439	-0.8327
8	0.5413	0.0101	0.6798	1.2066	-1.7379	3.3962	0.6817	-0.2578	-0.542	0.5481	0.2842	-0.1983	0.9284	-0.0265	0.9864	1.1645	-0.0692	-0.679	0.5196	0.0764	1.0782	-28.4677	-22.6924	8.0209
9	0.642	-0.7476	0.3083	0.8659	-0.2668	0.6943	0.3124	0.2915	-0.925	-0.084	0.2584	0.2	0.4321	0.448	0.0064	0.4513	0.0713	-0.1081	0.4306	-0.0843	0.6126	-13.3663	-13.9264	10.9906
10	0.1056	-0.118	-0.0902	0.3835	-0.2131	0.4402	0.564	0.5377	-0.3872	-0.7759	-0.08	0.5093	0.064	0.5237	-0.0008	0.5402	-0.0085	-0.1355	0.5707	-0.0998	0.5474	-19.4172	-9.847	1.0405
11	0.9989	0.5756	-0.7236	1.8926	0.6696	1.2227	0.2997	-0.792	-0.2909	0.6278	0.0609	0.6379	0.3212	-0.7049	-0.0011	0.7624	0.0174	-0.0374	0.5264	0.1233	0.783	-22.4955	-14.1984	16.1262
12	1.0182	0.3057	-0.0939	0.968	0.6357	0.5084	0.0946	-0.3362	-0.0458	0.4242	0.0264	0.2808	0.1599	-0.2277	0.0013	0.5382	-0.0203	0.0198	0.4959	-0.0162	0.5289	-17.5812	-7.7327	17.4201
13	0.5188	0.1978	0.2344	0.1207	0.1405	0.191	0.2307	-0.5359	-0.0626	0.0073	0.2344	0.7925	0.0777	-0.5515	-0.0233	0.5317	0.0815	0.124	0.5641	0.1336	0.706	-28.0203	-5.9077	12.1669
14	0.0843	0.0575	-0.0901	0.045	-0.0717	0.0909	0.0546	-0.6455	-0.7406	0.1598	0.6864	-0.3102	-0.0541	-0.1033	0.0065	0.9155	-0.1335	-0.1662	0.7392	0.1032	1.0063	-16.3176	-23.9915	23.6438
15	0.2611	0.1506	-0.4029	0.6635	0.5326	1.5837	0.3613	-0.343	-0.6055	0.4248	0.6299	0.5426	0.1046	0.0068	0.0501	0.663	-0.0145	-0.2401	0.3132	0.0675	1.102	-18.9946	-20.0352	15.6881

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 35 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 128 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 129 through 168 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 34 through 45 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 46 through 53 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 54 through 73 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 74 through 89 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 90 through 106 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 107 through 127 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 128 through 139 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 140 through 151 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 152 through 168 )

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