PDB-4dy5: Crystal structure of Salmonella Typhimurium PliG, a periplasmic l...

ID or keywords:

Entry

Database: PDB / ID: 4dy5

Title

Crystal structure of Salmonella Typhimurium PliG, a periplasmic lysozyme inhibitor of g-type lysozyme

Components

Gifsy-1 prophage protein

Keywords

HYDROLASE INHIBITOR / lysozyme inhibitor / g-type lysozyme binding

Function / homology

Jelly Rolls - #380 / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Jelly Rolls / Sandwich / Mainly Beta / Gifsy-1 prophage protein

Function and homology information

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Leysen, S. / Theuwis, V. / Vanderkelen, L. / Michiels, C.W. / Strelkov, S.V.

Citation

Journal: J.Struct.Biol. / Year: 2012
Title: Structural characterization of the PliG lysozyme inhibitor family.
Authors: Leysen, S. / Vanderkelen, L. / Van Asten, K. / Vanheuverzwijn, S. / Theuwis, V. / Michiels, C.W. / Strelkov, S.V.

History

Deposition	Feb 28, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 13, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 24, 2012	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4dy5.cif.gz	152.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4dy5.ent.gz	122.8 KB	Display	PDB format
PDBx/mmJSON format	4dy5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4dy5_validation.pdf.gz	448.9 KB	Display	wwPDB validaton report
Full document	4dy5_full_validation.pdf.gz	450.9 KB	Display
Data in XML	4dy5_validation.xml.gz	18.4 KB	Display
Data in CIF	4dy5_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dy/4dy5 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/4dy5	HTTPS FTP

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Related structure data

Related structure data	4dy3C 4dzgC C: citing same article (ref.)
Similar structure data	7jo8-2 1fkv-d 5m38-1 5m3g-3 1mzk-d 4ppt-d 3soe-d 3hqx-d 6pvx-1 2jjv-1 Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Gifsy-1 prophage protein

B: Gifsy-1 prophage protein

C: Gifsy-1 prophage protein

hetero molecules

37.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Gifsy-1 prophage protein

hetero molecules

defined by author&software
12.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Gifsy-1 prophage protein

hetero molecules

defined by author&software
12.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Gifsy-1 prophage protein

hetero molecules

defined by author&software
12.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	45.338, 89.199, 97.637
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Gifsy-1 prophage protein Mass: 12398.679 Da / Num. of mol.: 3 / Fragment: UNP residues 23-133 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: STM2610 / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q8ZMZ1
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.65 Å³/Da / Density % sol: 53.65 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH7.5, 20% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 24, 2011
Radiation	Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.78→19.79 Å / Num. all: 38815 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / R_sym value: 3.9 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.78→1.88 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.8 / R_sym value: 35.1 / % possible all: 92.3

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Processing

Software

Name	Version	Classification
XDS		data scaling
PHASER		phasing
PHENIX	(phenix.refine: 1.7.2_869)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.78→19.603 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 20.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.212	1915	5.01 %
R_work	0.1873	-	-
obs	0.1886	38202	98.69 %
all	-	38202	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 53.443 Å² / k_sol: 0.387 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.8093 Å²	0 Å²	0 Å²
2-	-	-2.145 Å²	0 Å²
3-	-	-	-0.6642 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→19.603 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2568	0	15	360	2943

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2677
X-RAY DIFFRACTION	f_angle_d	1.051	3606
X-RAY DIFFRACTION	f_dihedral_angle_d	15.048	1029
X-RAY DIFFRACTION	f_chiral_restr	0.078	377
X-RAY DIFFRACTION	f_plane_restr	0.004	474

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 (%)
1.78-1.8246	0.3193	121	0.3105	2200	X-RAY DIFFRACTION	84
1.8246-1.8739	0.2936	115	0.2419	2566	X-RAY DIFFRACTION	100
1.8739-1.929	0.2674	130	0.2248	2577	X-RAY DIFFRACTION	100
1.929-1.9912	0.2281	142	0.2099	2600	X-RAY DIFFRACTION	100
1.9912-2.0623	0.2487	113	0.1867	2632	X-RAY DIFFRACTION	100
2.0623-2.1447	0.2451	157	0.1883	2561	X-RAY DIFFRACTION	100
2.1447-2.2422	0.2344	151	0.1845	2579	X-RAY DIFFRACTION	100
2.2422-2.3602	0.2054	140	0.1872	2607	X-RAY DIFFRACTION	100
2.3602-2.5078	0.2092	131	0.1832	2635	X-RAY DIFFRACTION	100
2.5078-2.701	0.2218	151	0.1831	2610	X-RAY DIFFRACTION	100
2.701-2.972	0.233	141	0.1879	2619	X-RAY DIFFRACTION	100
2.972-3.4001	0.1866	148	0.1724	2645	X-RAY DIFFRACTION	100
3.4001-4.2764	0.1858	143	0.1643	2681	X-RAY DIFFRACTION	100
4.2764-19.604	0.195	132	0.1951	2775	X-RAY DIFFRACTION	98

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	2.6516	0.9865	-1.8053	1.1325	-1.3635	2.5027	-0.361	-0.0087	-0.3352	-0.1371	0.0498	-0.156	0.4963	-0.1194	0.0832	0.5144	0.2261	0.3331	0.4698	0.2056	0.3013	15.5218	-5.3666	-5.1851
2	1.5324	-0.6164	2.1397	0.4016	-0.2666	5.2297	0.0317	0.02	0.0793	0.2658	-0.1301	-0.3254	0.1733	0.5701	0.2479	0.2675	0.1374	-0.2232	0.9513	0.661	0.2092	23.5841	-2.8697	10.2702
3	3.142	-0.8186	2.991	2.6309	-2.9575	4.8263	-0.1081	-0.4995	-0.2625	0.2521	-0.5243	-0.4964	-0.0847	0.8839	0.3604	0.1642	-0.0014	0.0272	0.4221	0.2429	0.3236	17.2996	4.6405	-1.7041
4	1.502	0.2466	-0.3425	1.9546	-0.956	4.999	-0.5137	-0.246	-0.2951	0.2871	-0.2685	-0.111	0.7806	0.544	-0.0374	0.2034	-0.0105	0.13	0.1103	0.131	0.217	10.9922	-2.7815	-2.5625
5	2.7401	1.5539	-0.3959	2.8857	-2.0005	3.9226	0.0061	-0.3221	-0.0513	0.4241	-0.3838	-0.0868	0.167	0.1596	0.2375	0.2591	-0.0313	0.0544	0.1725	0.0091	0.1376	8.5957	1.3083	7.1225
6	2.7617	0.1785	0.1705	4.1792	-2.201	1.8435	0.0461	-0.2768	0.1413	0.6152	-0.1325	0.1826	0.1769	-0.5461	-0.0309	0.3346	-0.0893	0.1167	0.2401	-0.0327	0.1601	3.3105	0.1917	10.4758
7	1.7321	-0.7473	0.904	2.1793	1.3713	2.5654	-0.0728	-0.1205	-0.0886	-0.1876	-0.1784	0.0837	0.9463	0.1708	0.2086	0.2383	-0.0039	0.0924	0.1537	0.0155	0.2203	8.6495	-3.2951	0.5268
8	7.7235	0.7486	-3.8477	8.401	1.0318	7.621	0.0364	0.5606	0.6668	-0.5428	-0.2559	0.8157	-0.4132	-0.5825	0.0788	0.2243	-0.0058	-0.0952	0.1685	-0.0042	0.3214	2.6853	10.6274	-11.2568
9	0.6251	-0.7633	0.0743	4.1736	-4.0243	8.4524	0.0586	-0.4527	-0.2059	0.4448	-0.2278	-0.1968	-0.0962	0.1573	0.1223	0.1299	-0.0811	-0.0471	0.2756	0.1308	0.1887	15.0443	5.3558	3.2649
10	5.1907	-1.88	1.8414	1.9605	-1.8052	2.956	0.0764	0.0653	0.3148	0.0435	-0.2269	-1.193	-0.516	1.1337	0.204	0.3122	-0.0791	-0.0369	0.395	-0.0294	0.4766	33.5148	16.3	-12.1053
11	3.7011	1.0374	-0.4321	1.8587	-0.3656	2.1261	-0.1472	-0.0564	-0.2117	0.0964	0.021	-0.7749	-0.0926	0.285	0.1071	0.1225	-0.0073	0.0132	0.1302	0.002	0.1671	28.2266	9.2386	-12.81
12	4.8842	-2.0734	-1.3455	5.5156	-0.2405	4.0798	0.0498	0.1604	-0.209	-0.2631	-0.1617	0.0625	0.0792	0.0246	0.1065	0.1114	-0.0218	-0.0703	0.1219	0.0018	0.1115	21.7162	16.8815	-17.93
13	3.5806	1.8208	1.9823	6.107	-0.3281	7.2307	0.2628	0.493	-0.6491	-0.4039	0.2322	0.1454	0.0613	0.2555	-0.3002	0.1716	-0.0056	-0.0747	0.1465	-0.0252	0.1845	16.7626	13.2355	-21.6918
14	1.9066	-1.2484	-0.1109	4.6411	-0.2083	1.4874	-0.0314	0.0263	0.1062	-0.0777	-0.0356	-0.2128	-0.2291	-0.0006	0.0531	0.1397	-0.0373	-0.0226	0.1185	-0.0094	0.1453	20.7113	18.7344	-17.1566
15	3.0519	-0.1644	-0.409	8.5759	0.3283	2.0535	-0.222	0.2462	-0.2063	-0.5107	0.1075	0.0427	0.1634	-0.1306	0.0985	0.1512	-0.0288	0.0255	0.1733	-0.0276	0.1388	24.6252	4.1688	-18.6308
16	1.0916	0.7695	-0.2898	6.7372	3.073	4.3836	-0.1928	0.5452	-0.4105	-0.6741	0.3747	-1.0612	0.0237	0.7752	-0.1649	0.3844	-0.1626	0.143	0.5155	-0.1303	0.4826	48.746	-5.5054	-21.7772
17	3.3874	0.0152	0.7168	3.5474	2.2432	7.5784	-0.1109	0.0909	0.1001	0.0187	0.0408	-0.1555	-0.1158	0.2488	0.0171	0.1242	-0.0771	0.04	0.2233	-0.0635	0.2657	43.6309	-4.0626	-14.8247
18	3.9464	-0.2381	2.0257	4.7246	2.5045	5.493	0.1573	-0.1052	0.0062	0.4019	-0.0069	-0.2225	0.3725	0.1596	-0.0766	0.1656	-0.0812	0.0237	0.1694	-0.0372	0.17	38.7471	-13.1558	-18.639
19	3.742	0.6539	-1.9519	6.0143	-0.1783	6.194	0.1782	-0.273	0.1406	0.2898	-0.0208	0.2893	0.255	-0.0439	-0.1035	0.1642	-0.0457	-0.0269	0.1712	-0.0574	0.1732	33.2064	-15.1952	-21.1636
20	1.8505	-0.3501	0.4275	6.2282	4.9598	5.0133	-0.0796	-0.2586	0.392	-0.4471	0.1992	0.0581	-0.5572	0.1392	-0.1857	0.1238	-0.0655	0.0429	0.2256	-0.0335	0.191	38.3879	-5.075	-18.9752
21	4.6393	-1.0523	-2.9785	2.9114	1.1873	5.0139	-0.2591	0.1516	-0.2476	0.0626	0.076	0.2739	0.4727	-0.9552	0.4257	0.3859	-0.1883	0.2552	1.0891	-0.393	0.3188	32.8996	-2.4819	-0.9226
22	1.9394	0.3727	0.535	8.159	6.5082	5.5786	0.3007	0.412	-0.4032	0.2132	0.0174	-0.375	0.7346	0.2247	-0.377	0.228	0.0264	-0.0249	0.3001	-0.0959	0.2454	45.3924	-11.4966	-14.0285

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 23:28)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 29:36)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 37:45)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 46:56)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 57:77)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 78:104)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 105:113)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 114:122)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 123:133)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 24:36)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 37:56)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 57:81)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 82:91)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 92:113)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 114:133)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 24:36)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 37:56)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 57:76)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 77:104)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 105:113)
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 114:122)
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 123:133)

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