PDB-6ikk: Crystal structure of YfiB(L43P) in complex with YfiR

ID or keywords:

Entry

Database: PDB / ID: 6ikk

Title

Crystal structure of YfiB(L43P) in complex with YfiR

Components

YfiB
YfiR

Keywords

SIGNALING PROTEIN /

Complex / signalling system /

peptidoglycan binding

Function / homology

Function and homology information

cell outer membrane /

periplasmic space
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.19 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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

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Related structure data

Related structure data	6ikiC 6ikjC 4zhuS 4zhwS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5y61-1 1ot7-1 4zhy-d 2xnj-2 5h2u-2 5d7v-4 2ofc-d 5eb1-1 3b6q-d 3wg6-2 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	#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: YfiR

C: YfiB

D: YfiR

hetero molecules

78.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: YfiB

B: YfiR

hetero molecules

defined by author&software
Evidence: equilibrium centrifugation
39.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: YfiB

D: YfiR

hetero molecules

defined by author&software
39.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.798, 58.413, 70.324
Angle α, β, γ (deg.)	72.69, 83.01, 89.33
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
1	2	B
2	2	D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLN	GLN	PRO	PRO	A	A	44 - 166	44 - 166
2	1	GLN	GLN	PRO	PRO	C	C	44 - 166	44 - 166
1	2	THR	THR	ALA	ALA	B	B	39 - 184	39 - 184
2	2	THR	THR	ALA	ALA	D	D	39 - 184	39 - 184

NCS ensembles :

ID
1
2

#1: Protein	YfiB Mass: 18417.943 Da / Num. of mol.: 2 / Mutation: L43P 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: Protein	YfiR Mass: 20704.859 Da / Num. of mol.: 2 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: yfiR, PA1121 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I4L4
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.48 Å³/Da / Density % sol: 50.33 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10%(w/v) PEG 6000, 0.1 M Bicine pH 9.0

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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: 2.2→66.62 Å / Num. obs: 37342 / % possible obs: 97.7 % / Redundancy: 3.5 % / R_merge(I) obs: 0.089 / Net I/σ(I): 13
Reflection shell	Resolution: 2.2→2.27 Å / Redundancy: 3 % / R_merge(I) obs: 0.462 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1797 / % possible all: 95

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ZHU, 4ZHW

4zhu

4zhw

Resolution: 2.19→66.62 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.946 / SU B: 9.669 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20335	1999	5.4 %	RANDOM
R_work	0.17884	-	-	-
obs	0.18015	35314	96.91 %	-

Solvent computation

Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å

Displacement parameters

B_iso mean: 49.794 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.22 Å²	0.42 Å²	-0.96 Å²
2-	-	-0.08 Å²	0.38 Å²
3-	-	-	-0.11 Å²

Refinement step

Cycle: 1 / Resolution: 2.19→66.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4217	0	10	189	4416

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	4288
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4067
X-RAY DIFFRACTION	r_angle_refined_deg	1.543	1.964	5789
X-RAY DIFFRACTION	r_angle_other_deg	0.986	3	9363
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.282	5	541
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.815	22.667	210
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.448	15	742
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.834	15	58
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	645
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	4835
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	911
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.435	2.579	2176
X-RAY DIFFRACTION	r_mcbond_other	2.433	2.577	2175
X-RAY DIFFRACTION	r_mcangle_it	3.595	3.852	2713
X-RAY DIFFRACTION	r_mcangle_other	3.595	3.854	2714
X-RAY DIFFRACTION	r_scbond_it	3.496	2.924	2112
X-RAY DIFFRACTION	r_scbond_other	3.166	2.912	2105
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.645	4.236	3065
X-RAY DIFFRACTION	r_long_range_B_refined	7.98	31.325	4580
X-RAY DIFFRACTION	r_long_range_B_other	7.926	30.911	4540
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	7360	0.09
1	2	C	7360	0.09
2	1	B	8610	0.08
2	2	D	8610	0.08

LS refinement shell

Resolution: 2.193→2.25 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	133	-
R_work	0.258	2363	-
obs	-	-	86.79 %

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	7.1838	1.7226	3.143	1.932	0.4315	8.8256	-0.1237	0.161	0.4622	-0.4502	0.1072	-0.0401	0.0064	0.2696	0.0165	0.1791	0.0091	0.0423	0.0887	-0.0668	0.2594	23.24	-21.492	40.409
2	13.8203	-2.543	8.0286	0.6704	-2.5315	10.2766	-0.0488	0.5592	0.55	0.1208	-0.0992	-0.0944	-0.6469	0.2779	0.148	0.3773	-0.0006	-0.012	0.1843	0.0202	0.1822	1.893	-22.463	23.028
3	14.8549	-2.5566	10.7898	5.5914	-6.6118	12.5845	-0.081	-0.2138	1.4312	-0.6556	-0.2927	0.0624	0.366	0.1156	0.3737	0.4045	-0.0537	0.1552	0.3215	0.0125	0.5576	16.778	-22.999	25.079
4	7.4888	-0.919	2.4884	2.015	-0.0562	6.0256	0.1114	0.1186	-0.2791	-0.1251	0.1029	0.0441	0.0817	-0.102	-0.2143	0.2329	-0.0064	0.0115	0.0831	-0.0187	0.099	3.425	-31.018	26.943
5	3.163	2.6479	-0.4873	4.9884	-0.538	1.508	0.0677	-0.3762	-0.1977	0.2211	-0.0874	-0.31	0.0666	0.2426	0.0197	0.1183	0.0129	-0.0261	0.1332	-0.0364	0.1478	16.959	-33.616	52.218
6	5.8426	0.5008	-0.5657	1.5616	-0.3818	2.0985	0.2312	-0.818	0.0325	0.3992	-0.1676	0.0214	-0.1428	0.2487	-0.0636	0.1926	-0.0417	0.0096	0.1776	-0.0725	0.1628	13.17	-29.531	58.608
7	1.0997	-0.2299	-0.3016	0.7309	0.6686	5.6961	-0.021	-0.103	-0.1927	0.1575	-0.0307	0.2174	-0.1537	-0.2031	0.0517	0.2073	0.0546	0.0895	0.1999	-0.0489	0.4629	5.87	-30.897	52.247
8	4.4439	-2.0849	-1.8342	6.2956	-0.1086	3.3881	0.1588	0.0556	-0.2055	0.1319	-0.2827	0.7246	0.3199	-0.5606	0.1238	0.1514	-0.0609	0.0309	0.2023	-0.0954	0.1576	1.748	-29.617	47.265
9	0.5863	-0.1987	0.1421	7.2576	-7.5678	7.9054	0.0032	0.0298	-0.1142	-0.5521	0.6941	0.7144	0.614	-0.7455	-0.6973	0.4243	-0.0584	-0.0459	0.4308	-0.0677	0.3966	7.032	-37.297	42.103
10	7.2076	-4.5303	-4.4213	13.9806	-2.0381	9.0518	-0.1994	0.0817	-0.6026	-0.1175	-0.1719	-0.6637	1.108	0.9222	0.3712	0.3224	0.1266	-0.0322	0.2345	-0.1146	0.2817	17.82	-41.596	43.835
11	6.7438	-1.1606	0.2445	0.4398	-0.1435	4.5784	0.0752	0.2408	0.057	-0.1031	-0.0428	0.0176	-0.2242	0.2129	-0.0325	0.163	-0.0292	-0.0037	0.0327	-0.0123	0.1561	13.058	-27	39.058
12	1.4529	-0.72	-1.7131	16.3715	-3.875	6.3791	-0.0468	0.2156	-0.3614	-0.1068	-0.0671	-0.3326	0.4949	0.6404	0.1139	0.2195	0.0922	-0.0013	0.3461	-0.1396	0.308	23.7	-32.544	38.625
13	5.1225	3.3889	3.1521	4.6539	2.1361	10.0694	0.1246	-0.6354	0.2032	0.162	-0.1887	0.1183	0.2922	-0.1319	0.0641	0.0837	0.0787	0.0549	0.228	0.0236	0.1429	-4.847	-61.579	77.655
14	5.3374	3.8053	6.5631	5.7912	3.7616	12.2479	0.2308	-0.8159	-0.4501	0.3345	-0.2524	0.1856	0.6174	-1.1341	0.0216	0.1386	-0.0003	0.0993	0.2215	0.1388	0.3857	-17.811	-73.705	56.255
15	5.3391	3.021	2.7194	17.5342	7.1646	9.4386	0.1878	-0.4262	-0.1472	0.4237	-0.2438	0.5749	0.9145	-0.0588	0.056	0.1791	0.0063	0.0619	0.4003	0.0852	0.2734	-18.425	-67.782	70.269
16	5.3491	-1.6189	-2.6445	4.5188	6.1315	13.3679	0.029	-0.0891	0.1659	-0.2673	-0.2103	0.152	-0.5733	-0.6118	0.1813	0.0748	0.0175	-0.0149	0.0577	0.0392	0.1909	-16.543	-61.69	56.475
17	5.7437	-0.9485	-1.9319	3.6167	4.0562	10.1523	-0.042	-0.4028	0.0985	-0.1352	-0.1495	0.2302	-0.3455	-0.5263	0.1915	0.0651	0.0663	-0.0085	0.1158	-0.0294	0.215	-23.027	-63.291	56.257
18	4.8712	-1.8713	-0.5185	4.0781	2.412	6.0174	0.0135	0.1348	-0.0198	-0.3396	0.0275	-0.0253	0.0224	0.1173	-0.0411	0.0872	0.0071	0.0394	0.01	0.0133	0.1253	-9.448	-66.989	52.434
19	1.9403	0.5348	-0.2703	2.809	-1.9659	5.6112	0.0472	-0.4337	0.2781	0.1306	-0.0857	-0.1441	-0.4225	0.4069	0.0385	0.1208	0.0183	0.0012	0.1669	-0.064	0.1499	4.887	-49.695	68.681
20	3.6983	-0.6251	-1.5937	2.1558	-0.2818	5.2798	0.0158	-0.3121	-0.0235	-0.158	-0.1011	-0.2354	0.1334	0.772	0.0853	0.1205	0.0205	0.0018	0.1418	-0.0007	0.1832	9.843	-54.403	63.812
21	5.0792	-1.7997	0.1474	3.1284	-1.6977	11.0469	0.0267	0.556	-0.2411	-0.6747	0.0187	0.1753	0.9665	0.2204	-0.0454	0.2537	-0.009	-0.0105	0.1223	-0.0517	0.2018	3.265	-59.771	55.536
22	3.853	6.2402	-0.8982	10.3972	-1.1897	0.4595	-0.4685	0.3088	0.429	-0.8534	0.4924	0.7402	0.019	-0.057	-0.0239	0.3459	0.0202	-0.0051	0.2697	0.0055	0.3279	-4.936	-52.705	57.157
23	2.0383	0.4067	-0.1159	8.7124	0.8356	0.8369	-0.0637	-0.1745	0.2926	0.0227	0.0529	0.2054	-0.1704	-0.144	0.0108	0.1349	0.0452	-0.0097	0.1587	-0.0217	0.1854	-7.361	-51.09	65.278
24	4.3182	-0.8103	0.5589	6.9168	4.9008	7.0442	0.0713	-0.5863	0.2751	0.1459	-0.2264	0.1158	-0.2057	-0.5293	0.1551	0.1053	0.0657	0.0337	0.1781	0.009	0.1242	-6.894	-58.99	71.392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	44 - 61
2	X-RAY DIFFRACTION	2	A	62 - 73
3	X-RAY DIFFRACTION	3	A	74 - 90
4	X-RAY DIFFRACTION	4	A	91 - 167
5	X-RAY DIFFRACTION	5	B	38 - 81
6	X-RAY DIFFRACTION	6	B	82 - 105
7	X-RAY DIFFRACTION	7	B	106 - 119
8	X-RAY DIFFRACTION	8	B	120 - 139
9	X-RAY DIFFRACTION	9	B	140 - 150
10	X-RAY DIFFRACTION	10	B	151 - 160
11	X-RAY DIFFRACTION	11	B	161 - 177
12	X-RAY DIFFRACTION	12	B	178 - 186
13	X-RAY DIFFRACTION	13	C	43 - 61
14	X-RAY DIFFRACTION	14	C	62 - 73
15	X-RAY DIFFRACTION	15	C	74 - 90
16	X-RAY DIFFRACTION	16	C	91 - 106
17	X-RAY DIFFRACTION	17	C	107 - 139
18	X-RAY DIFFRACTION	18	C	140 - 167
19	X-RAY DIFFRACTION	19	D	39 - 84
20	X-RAY DIFFRACTION	20	D	85 - 119
21	X-RAY DIFFRACTION	21	D	120 - 139
22	X-RAY DIFFRACTION	22	D	140 - 150
23	X-RAY DIFFRACTION	23	D	151 - 170
24	X-RAY DIFFRACTION	24	D	171 - 185

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Assembly

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Experiment

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About Yorodumi

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi