PDB-4wlk: Stationary Phase Survival Protein YuiC from B.subtilis complexed ...

ID or keywords:

Entry

Database: PDB / ID: 4wlk

Title

Stationary Phase Survival Protein YuiC from B.subtilis complexed with reaction product

Components

YuiC

Keywords

LYASE / lytic transglycosylase / peptidoglycan remodelling / stationary phase / MltA

Function / homology

: / 3D domain / 3D domain / RlpA-like domain superfamily / peptidoglycan turnover / outer membrane / hydrolase activity, hydrolyzing O-glycosyl compounds / Chem-3QL / Uncharacterized protein YuiC

Function and homology information

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.03 Å

Authors

Quay, D.H.X. / Cole, A.R. / Cryar, A. / Thalassinos, K. / Williams, M.A. / Bhakta, S. / Keep, N.H.

Citation

Journal: Bmc Struct.Biol. / Year: 2015
Title: Structure of the stationary phase survival protein YuiC from B.subtilis.
Authors: Quay, D.H. / Cole, A.R. / Cryar, A. / Thalassinos, K. / Williams, M.A. / Bhakta, S. / Keep, N.H.

History

Deposition	Oct 7, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 21, 2016	Group: Database references
Revision 1.2	Jan 10, 2024	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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Download

PDBx/mmCIF format	4wlk.cif.gz	132.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4wlk.ent.gz	104.2 KB	Display	PDB format
PDBx/mmJSON format	4wlk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4wlk_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4wlk_full_validation.pdf.gz	1 MB	Display
Data in XML	4wlk_validation.xml.gz	14.1 KB	Display
Data in CIF	4wlk_validation.cif.gz	19.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/4wlk ftp://data.pdbj.org/pub/pdb/validation_reports/wl/4wlk	HTTPS FTP

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Related structure data

Related structure data	4wjtSC 4wliC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4wjt-d 4wli-1 6uvf-5 3i17-d 6hnk-d 1t2w-4 1qxh-d 6hnj-d 5v7b-d 5xxr-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

Deposited unit

A: YuiC

B: YuiC

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	147.210, 147.210, 37.870
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	YuiC Mass: 18477.783 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yuiC, BSU32070 / Plasmid: pNic28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta-2 / References: UniProt: O32108
#2: Chemical	ChemComp-3QL / N-[(1R,2S,3R,4R,5R)-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-6,8-dioxabicyclo[3.2.1]octan-4-yl]ethanamide Mass: 406.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₂₆N₂O₁₀
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.14 Å³/Da / Density % sol: 42.44 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 40% glycerol ethoxylate / PH range: Not buffered

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.03→42.5 Å / Num. obs: 19631 / % possible obs: 99.4 % / Redundancy: 3.8 % / R_sym value: 0.122 / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.03→2.08 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.576 / Mean I/σ(I) obs: 2.2 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
PHASER		phasing
Aimless		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4WJT

4wjt

Resolution: 2.03→42.496 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2051	968	4.93 %
R_work	0.1717	-	-
obs	0.1733	19628	99.36 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.03→42.496 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2265	0	56	178	2499

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2384
X-RAY DIFFRACTION	f_angle_d	0.795	3250
X-RAY DIFFRACTION	f_dihedral_angle_d	12.435	893
X-RAY DIFFRACTION	f_chiral_restr	0.033	376
X-RAY DIFFRACTION	f_plane_restr	0.002	406

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 (%)
2.0304-2.1375	0.2864	145	0.2685	2635	X-RAY DIFFRACTION	99
2.1375-2.2714	0.2424	143	0.2281	2646	X-RAY DIFFRACTION	98
2.2714-2.4468	0.2275	125	0.1949	2667	X-RAY DIFFRACTION	99
2.4468-2.693	0.2159	155	0.1774	2658	X-RAY DIFFRACTION	100
2.693-3.0825	0.1976	125	0.165	2691	X-RAY DIFFRACTION	100
3.0825-3.8833	0.2147	135	0.1593	2681	X-RAY DIFFRACTION	100
3.8833-42.5052	0.1631	140	0.1409	2682	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	0.4152	-0.0579	0.2964	0.0329	-0.0788	0.2811	0.1838	0.6488	-0.2967	0.0389	0.0352	0.0023	0.571	1.152	0.0092	0.3139	0.0635	-0.0309	0.5453	-0.131	0.4861	-5.3605	16.8938	-8.5428
2	0.1046	0.0369	-0.1081	0.6916	-0.0215	0.3147	0.0231	-0.0304	-0.1979	0.0836	-0.0113	0.1705	-0.1154	0.0638	-0.0001	0.1758	-0.016	0.0022	0.2319	-0.007	0.1828	-25.3888	24.0565	3.9513
3	0.3169	0.1095	-0.1222	0.1877	-0.1681	0.1456	0.0173	0.0749	0.0547	-0.1008	0.1731	-0.0372	-0.1524	0.1753	0	0.1911	-0.0127	0.0064	0.2331	0	0.2225	-24.7725	29.4783	-3.3819
4	0.7059	-0.197	-0.4122	0.4312	-0.1652	0.45	0.0728	-0.0353	-0.1245	0.1682	-0.0947	-0.2199	-0.0354	0.1089	0	0.1803	-0.0315	-0.0382	0.1903	0.0146	0.143	-16.5168	26.217	2.7615
5	0.156	-0.0105	0.0735	0.0788	-0.0627	0.0718	-0.0264	0.1415	0.2444	0.0079	-0.1965	-0.0314	-0.0897	-0.0262	0.0053	0.2007	-0.0336	-0.0424	0.1763	-0.0168	0.2552	-23.9201	20.4972	1.5015
6	0.0303	-0.01	0.0284	0.1035	0.0235	0.0359	-0.0418	0.203	-0.3662	-0.2269	-0.1414	-0.1387	-0.1955	-0.1975	0.0001	0.1924	-0.0155	-0.012	0.2453	-0.0264	0.284	-28.6522	11.9152	-0.59
7	0.0324	0.1526	-0.0361	0.631	-0.1323	0.2126	-0.1106	0.1061	0.1458	0.2204	0.2201	-0.6366	-0.0568	0.0202	-0.0007	0.2535	0.0344	0.0477	0.2772	-0.0177	0.2847	-20.0647	0.2502	4.8833
8	0.4439	0.0563	0.0656	0.1883	-0.1749	0.2781	-0.1085	-0.3877	-0.3577	0.4263	0.0078	0.2372	0.5183	-0.1629	0.0007	0.339	0.0096	0.0716	0.2569	0.02	0.2824	-35.383	-10.4943	17.6837
9	0.1749	0.3927	-0.0455	0.8662	-0.1065	0.0149	-0.0747	-0.2542	0.3132	0.2119	-0.0206	0.3176	0.0274	0.7215	0.0206	0.2993	0.0593	-0.0436	0.4695	-0.0684	0.292	-26.6874	-0.3248	25.846
10	0.2066	0.2816	-0.4515	0.4205	-0.4519	2.1263	-0.3609	-0.045	0.4051	0.1138	0.1651	-0.3892	0.2665	0.5582	-0.1117	0.2453	0.1154	-0.0983	0.3977	-0.061	0.4351	-15.5788	-7.578	18.1889
11	0.6334	0.0426	-0.2151	0.0682	-0.1546	0.6991	0.0338	0.2484	0.0157	-0.0903	-0.0731	0.0896	0.0415	-0.0651	-0.0209	0.1409	0.0309	-0.0011	0.1562	-0.0073	0.1653	-34.8153	2.6267	6.2689
12	0.1442	-0.0659	0.1046	0.1505	-0.0884	0.0879	-0.0103	0.1894	-0.25	0.1928	0.2133	-0.0777	-0.0661	0.0855	0.0022	0.1655	0.024	0.0203	0.1716	0.0012	0.213	-39.501	-1.3128	12.2576
13	0.1332	-0.248	-0.1342	0.5735	0.2921	0.1908	-0.1033	-0.0809	-0.0707	0.0318	0.0921	0.0214	0.1391	0.1282	0	0.1476	0.0222	0.0219	0.1648	-0.0172	0.1571	-29.5336	-5.581	10.3547
14	0.2873	0.1976	-0.0855	0.2605	-0.086	0.0329	-0.102	0.4218	0.1709	-0.2188	0.342	-0.1015	0.3699	0.0825	0.0007	0.2712	-0.0064	0.0124	0.276	-0.0082	0.2539	-32.4072	-3.0939	-1.8816
15	0.0074	-0.0462	-0.022	0.8258	0.2195	0.0732	-0.1983	0.0003	-0.0677	0.1761	-0.0332	0.319	-0.1324	0.11	-0.0156	0.1334	-0.0191	-0.0047	0.1762	-0.0364	0.1893	-30.8464	4.1226	8.6799
16	0.0605	0.0363	-0.0166	0.0269	-0.0273	0.0557	-0.1155	-0.2699	0.3102	0.3006	0.0176	-0.1876	-0.2527	-0.0644	0	0.261	-0.0348	-0.0154	0.2653	-0.0179	0.2867	-27.8857	13.4065	10.9062
17	0.1599	-0.0395	-0.1782	0.2285	0.1939	0.2754	0.1979	-0.048	-0.1538	0.1524	-0.0977	0.1616	0.1011	0.115	0.0014	0.1989	-0.0319	-0.0493	0.3262	0.0355	0.2948	-13.7524	15.0467	5.1452
18	0.5104	-0.3469	0.4891	0.2827	-0.099	1.6085	-0.1868	0.1598	0.5833	-0.345	0.0217	-0.2214	-0.7726	0.1504	-0.0593	0.3102	-0.048	0.0036	0.2806	0.0247	0.4302	-13.2398	35.4209	-1.3886
19	0.2312	-0.2215	0.041	0.2605	0.0366	0.1281	0.1074	0.3577	-0.107	-0.0847	-0.2292	0.0487	-0.1048	-0.0287	-0.0041	0.2874	-0.0277	0.0133	0.3674	0.0515	0.2026	-18.8329	32.7813	-12.0447
20	0.2072	0.1375	-0.231	0.1424	-0.3133	0.7611	0.1575	0.0575	-0.2345	-0.2865	-0.3508	0.1837	0.1465	0.4513	-0.0304	0.3085	0.0622	0.0059	0.321	-0.0646	0.2652	-17.9041	20.6945	-15.585

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 72 through 82 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 83 through 110 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 111 through 122 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 123 through 159 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 160 through 167 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 168 through 174 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 175 through 184 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 185 through 203 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 204 through 216 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 73 through 82 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 83 through 110 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 111 through 120 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 121 through 151 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 152 through 159 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 160 through 167 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 168 through 174 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 175 through 184 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 185 through 193 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 194 through 203 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 204 through 216 )

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