PDB-4s3j: Crystal structure of the Bacillus cereus spore cortex-lytic enzym...

ID or keywords:

Entry

Database: PDB / ID: 4s3j

Title

Crystal structure of the Bacillus cereus spore cortex-lytic enzyme SleL

Components

Cortical-lytic enzyme

Keywords

HYDROLASE / TIM Barrel / N-acetylglucosaminidase / Spore cortex

Function / homology

Chitinase A; domain 3 - #10 / Chitinase A; domain 3 / Glycosidases / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta / :

Function and homology information

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Christie, G. / Chirgadze, D.Y. / Ustok, F.I.

Citation

Journal: Proteins / Year: 2015
Title: Structural and functional analysis of SleL, a peptidoglycan lysin involved in germination of Bacillus spores.
Authors: Ustok, F.I. / Chirgadze, D.Y. / Christie, G.

History

Deposition	Feb 4, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 19, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 23, 2015	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	4s3j.cif.gz	744.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4s3j.ent.gz	630.3 KB	Display	PDB format
PDBx/mmJSON format	4s3j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4s3j_validation.pdf.gz	455.8 KB	Display	wwPDB validaton report
Full document	4s3j_full_validation.pdf.gz	463.3 KB	Display
Data in XML	4s3j_validation.xml.gz	57.6 KB	Display
Data in CIF	4s3j_validation.cif.gz	88.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s3/4s3j ftp://data.pdbj.org/pub/pdb/validation_reports/s3/4s3j	HTTPS FTP

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Related structure data

Related structure data	4s3kC 3cz8S 4f55 4fet C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1n59-1 2gt9-1 4zfz-2 1bhm-d 3p8v-d 2x70-1 6apn-2 5gsb-d 5ttk-4 5ynj-d 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: Cortical-lytic enzyme

B: Cortical-lytic enzyme

C: Cortical-lytic enzyme

hetero molecules

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

1

A: Cortical-lytic enzyme

hetero molecules

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

2

B: Cortical-lytic enzyme

hetero molecules

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

3

C: Cortical-lytic enzyme

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.330, 62.730, 119.880
Angle α, β, γ (deg.)	92.70, 100.99, 108.39
Int Tables number	1
Space group name H-M	P1

#1: Protein	Cortical-lytic enzyme / LysM domain protein Mass: 48530.141 Da / Num. of mol.: 3 / Fragment: UNP residues 2-430 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10876 / Gene: bcere0002_33520, DJ50_4346 / Plasmid: pNZ / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: C2N467
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1336 / 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: 2.45 Å³/Da / Density % sol: 49.86 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M trisodium citrate buffer, pH 5.5, 20% (w/v) PEG 3,000, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2013
Radiation	Monochromator: Si(111) single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. all: 182930 / Num. obs: 169576 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / B_iso Wilson estimate: 17.2 Å² / R_merge(I) obs: 0.064 / R_sym value: 0.064 / Net I/σ(I): 18.74
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.52 / Mean I/σ(I) obs: 3.4 / Num. unique all: 13527 / R_sym value: 0.52 / % possible all: 78.3

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Processing

Software

Name	Version	Classification
GDA		data collection
PHENIX	(phenix.refine: 1.9_1692)	model building
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX	1.9_1692	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3CZ8

3cz8

Resolution: 1.6→47.811 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 18.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1767	1942	1.18 %	Random
R_work	0.1568	-	-	-
obs	0.157	164510	89.96 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→47.811 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10143	0	12	1336	11491

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	10398
X-RAY DIFFRACTION	f_angle_d	1.18	14128
X-RAY DIFFRACTION	f_dihedral_angle_d	12.482	3832
X-RAY DIFFRACTION	f_chiral_restr	0.05	1568
X-RAY DIFFRACTION	f_plane_restr	0.007	1820

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 (%)
1.6-1.6391	0.2555	110	0.2183	8932	X-RAY DIFFRACTION	69
1.6391-1.6834	0.245	120	0.2029	10262	X-RAY DIFFRACTION	80
1.6834-1.733	0.2339	130	0.1923	10838	X-RAY DIFFRACTION	84
1.733-1.7889	0.2052	134	0.1859	11374	X-RAY DIFFRACTION	88
1.7889-1.8529	0.2045	142	0.18	11685	X-RAY DIFFRACTION	91
1.8529-1.9271	0.2049	137	0.1781	11731	X-RAY DIFFRACTION	91
1.9271-2.0148	0.2105	139	0.1733	11461	X-RAY DIFFRACTION	89
2.0148-2.121	0.1914	143	0.166	12134	X-RAY DIFFRACTION	94
2.121-2.2539	0.1902	149	0.1587	12361	X-RAY DIFFRACTION	96
2.2539-2.4279	0.1826	148	0.1528	12354	X-RAY DIFFRACTION	96
2.4279-2.6722	0.1506	147	0.1494	12262	X-RAY DIFFRACTION	95
2.6722-3.0588	0.158	144	0.1502	12070	X-RAY DIFFRACTION	93
3.0588-3.8535	0.1495	150	0.1446	12631	X-RAY DIFFRACTION	98
3.8535-47.8323	0.1672	149	0.1428	12473	X-RAY DIFFRACTION	97

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	1.5227	0.7395	0.0669	0.9314	0.1248	1.4285	-0.0367	-0.0749	-0.0578	0.0026	-0.0331	0.2096	-0.1181	-0.1479	-0.0007	0.0986	0.0344	-0.0567	0.1843	-0.0236	0.172	-27.1288	-1.308	94.6259
2	0.3641	0.2112	-0.0605	0.5537	-0.0162	0.4979	0.1171	-0.0619	-0.0359	0.2244	-0.1348	0.0856	0.0307	-0.066	0.0021	0.1619	-0.0501	-0.0053	0.1775	0.0111	0.1223	-24.1598	2.4731	109.7693
3	0.4079	0.1366	0.0811	0.7015	0.1503	0.5051	0.1583	-0.0622	0.0965	0.2978	-0.2088	0.1175	-0.1462	0.0215	0.043	0.3045	-0.0771	0.0349	0.1813	-0.0172	0.1556	-14.6073	32.7632	115.5893
4	0.3997	0.1435	-0.178	0.8327	0.072	0.7396	0.1183	-0.0108	-0.0642	0.238	-0.1471	-0.0497	-0.0538	0.0531	0.0049	0.1169	-0.0262	-0.0262	0.1378	0.0087	0.1132	-12.5231	11.4261	106.3585
5	0.9827	0.3895	0.1483	0.5935	0.0944	0.1859	0.0634	0.2555	0.0293	-0.2301	0.0044	0.1513	-0.0297	-0.1368	-0.0301	0.1539	0.1109	-0.0913	0.2358	0.0151	0.199	-13.4456	63.1698	63.1321
6	0.1758	-0.0843	-0.049	1.2115	-0.2757	0.4368	0.0865	0.067	0.0122	-0.1801	-0.0695	0.0316	-0.0345	-0.0491	-0.0103	0.1294	0.0609	-0.0036	0.1649	0.0198	0.1755	1.8011	57.8124	64.7751
7	0.5867	-0.042	0.1547	0.6634	-0.0395	0.5542	0.0529	0.0143	-0.1711	-0.1028	-0.0857	0.0244	0.1048	0.0035	0.0273	0.1153	0.0375	-0.0318	0.1482	0.0009	0.2015	6.6774	27.1727	75.2002
8	0.2422	-0.1072	-0.0617	0.189	0.094	0.1383	0.0047	-0.0742	-0.0516	0.0073	-0.0227	-0.072	0.0382	0.0302	0.0086	0.0034	0.061	-0.0557	0.1329	0.0084	0.1887	7.4307	45.3798	82.3445
9	0.1934	-0.0608	0.0438	0.1865	-0.0748	0.1891	0.0525	0.0403	-0.0354	-0.1142	-0.0724	0.0771	0.0392	-0.0601	-0.0165	-0.0136	0.0777	-0.0584	0.1551	-0.0107	0.1583	-6.6454	52.3257	75.1029
10	0.2368	0.1362	0.2826	1.273	0.4983	0.4528	-0.0473	-0.0489	-0.1856	-0.1992	0.0728	0.04	0.0937	-0.0274	-0.0363	0.4406	-0.0181	0.103	0.1781	0.0444	0.2347	-31.1309	21.2738	45.3132
11	0.2678	0.0524	-0.1418	0.4744	-0.0181	0.1413	0.0305	0.0026	0.0118	-0.1438	0.026	0.0211	0.1099	-0.0043	0.0855	0.7555	-0.1242	0.1881	0.1992	-0.0479	0.2623	-24.5419	25.1647	31.0966
12	0.3137	0.1984	-0.1977	0.7642	-0.2491	0.6089	-0.0727	-0.016	-0.058	-0.0105	-0.0142	-0.0514	-0.1742	0.1294	-0.185	0.6754	-0.1447	0.2433	0.2457	-0.0591	0.3133	-2.7077	48.068	35.2415
13	0.1999	0.0118	-0.1556	0.2818	-0.2064	0.6505	-0.0349	0.004	-0.0326	-0.0568	-0.0109	-0.0442	-0.0143	0.0835	-0.045	0.7649	-0.1603	0.2829	0.2693	-0.0669	0.3305	0.1434	49.6417	25.0819
14	0.3721	0.0956	-0.2072	0.0915	-0.1394	0.2253	-0.0095	0.0466	0.0175	-0.1212	0.0685	-0.0646	-0.0659	0.0157	0.1683	0.7788	-0.1322	0.2092	0.2187	-0.0289	0.2277	-18.6716	46.8185	25.4878
15	0.3886	0.234	-0.4139	0.2108	-0.1055	0.8807	-0.0162	0.0874	0.0205	-0.2967	0.0602	-0.0139	-0.0795	-0.0134	-0.058	0.5747	-0.0871	0.1331	0.1618	-0.0162	0.1991	-24.1462	45.6312	32.3315
16	0.4268	-0.1622	0.0279	0.2421	0.1476	0.1481	-0.1061	0.0242	-0.0443	-0.3568	0.1212	-0.0431	0.0945	-0.0217	0.1082	0.512	-0.0618	0.1204	0.142	-0.0215	0.1889	-26.8634	35.9751	39.0125

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 5:35 )	A	5 - 35
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 36:123 )	A	36 - 123
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 124:295 )	A	124 - 295
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 296:430 )	A	296 - 430
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 5:60 )	B	5 - 60
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 61:123 )	B	61 - 123
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 124:244 )	B	124 - 244
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 245:334 )	B	245 - 334
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 335:432 )	B	335 - 432
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 6:60 )	C	6 - 60
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 61:123 )	C	61 - 123
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 124:196 )	C	124 - 196
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 197:244 )	C	197 - 244
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 245:302 )	C	245 - 302
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 303:344 )	C	303 - 344
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 345:430 )	C	345 - 430

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