PDB-8y6t: Chitinase TfeC from Yersinia pseudotuberculosis

ID or keywords:

Entry

Database: PDB / ID: 8y6t

Title

Chitinase TfeC from Yersinia pseudotuberculosis

Components

DUF3142 domain-containing protein

Keywords

HYDROLASE / Chitinase

Function / homology

L(+)-TARTARIC ACID / :

Function and homology information

Biological species

Yersinia pseudotuberculosis B-6862 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Cui, R. / Li, D.F.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Structure of chitinase at 1.9 Angstroms resolution.
Authors: Cui, R. / Li, D.F.

History

Deposition	Feb 3, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8y6t.cif.gz	372.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8y6t.ent.gz	302.4 KB	Display	PDB format
PDBx/mmJSON format	8y6t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8y6t_validation.pdf.gz	482.4 KB	Display	wwPDB validaton report
Full document	8y6t_full_validation.pdf.gz	492.7 KB	Display
Data in XML	8y6t_validation.xml.gz	46.4 KB	Display
Data in CIF	8y6t_validation.cif.gz	64.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y6/8y6t ftp://data.pdbj.org/pub/pdb/validation_reports/y6/8y6t	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: DUF3142 domain-containing protein

B: DUF3142 domain-containing protein

C: DUF3142 domain-containing protein

D: DUF3142 domain-containing protein

hetero molecules

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

1

A: DUF3142 domain-containing protein

hetero molecules

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

2

B: DUF3142 domain-containing protein

hetero molecules

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

3

C: DUF3142 domain-containing protein

hetero molecules

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

4

D: DUF3142 domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.891, 63.849, 77.854
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	1
Space group name H-M	P1

#1: Protein	DUF3142 domain-containing protein Mass: 29920.240 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pseudotuberculosis B-6862 (bacteria) Gene: EGX52_02760 / Production host: Escherichia (bacteria) / References: UniProt: A0A3G5J269
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 858 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.91 Å³/Da / Density % sol: 35.47 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 0.2M Potassium Na tartrate tetrahydrate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 26, 2021
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 1.9→49.37 Å / Num. obs: 66146 / % possible obs: 94.93 % / Redundancy: 3.5 % / R_merge(I) obs: 0.119 / R_rim(I) all: 0.141 / Net I/σ(I): 1.97
Reflection shell	Resolution: 1.9→1.968 Å / Num. unique obs: 5147 / R_rim(I) all: 0.394

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
Aimless		data scaling
PDB_EXTRACT	3.27	data extraction
PHASER	2.7.0	phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→49.37 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 29.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2884	3179	4.81 %
R_work	0.2414	-	-
obs	-	66146	94.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→49.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6865	0	40	858	7763

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7090
X-RAY DIFFRACTION	f_angle_d	0.931	9679
X-RAY DIFFRACTION	f_dihedral_angle_d	5.098	4123
X-RAY DIFFRACTION	f_chiral_restr	0.058	1061
X-RAY DIFFRACTION	f_plane_restr	0.006	1245

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 (%)
1.9-1.9284	0.3184	114	0.2884	1899	X-RAY DIFFRACTION	67
1.9284-1.9585	0.2884	74	0.2782	2259	X-RAY DIFFRACTION	77
1.9585-1.9906	0.3251	159	0.255	2639	X-RAY DIFFRACTION	92
1.9906-2.025	0.3362	157	0.2567	2761	X-RAY DIFFRACTION	96
2.025-2.0618	0.316	159	0.2437	2770	X-RAY DIFFRACTION	96
2.0618-2.1014	0.2695	128	0.2456	2766	X-RAY DIFFRACTION	96
2.1014-2.1443	0.2975	134	0.2485	2790	X-RAY DIFFRACTION	97
2.1443-2.191	0.2869	157	0.2487	2811	X-RAY DIFFRACTION	97
2.191-2.2419	0.3158	152	0.2492	2736	X-RAY DIFFRACTION	97
2.2419-2.298	0.3241	123	0.2555	2854	X-RAY DIFFRACTION	97
2.298-2.3601	0.3676	133	0.2466	2759	X-RAY DIFFRACTION	97
2.3601-2.4296	0.3418	140	0.2524	2807	X-RAY DIFFRACTION	97
2.4296-2.508	0.2997	178	0.2471	2772	X-RAY DIFFRACTION	97
2.508-2.5976	0.3233	112	0.2592	2789	X-RAY DIFFRACTION	97
2.5976-2.7016	0.3019	158	0.2525	2861	X-RAY DIFFRACTION	98
2.7016-2.8246	0.3232	127	0.2606	2818	X-RAY DIFFRACTION	98
2.8246-2.9735	0.2897	145	0.2406	2774	X-RAY DIFFRACTION	98
2.9735-3.1597	0.3417	166	0.2405	2842	X-RAY DIFFRACTION	98
3.1597-3.4036	0.3103	107	0.2398	2853	X-RAY DIFFRACTION	98
3.4036-3.7461	0.2383	148	0.2223	2838	X-RAY DIFFRACTION	98
3.7461-4.2878	0.243	147	0.2185	2821	X-RAY DIFFRACTION	99
4.2878-5.4012	0.2433	149	0.214	2845	X-RAY DIFFRACTION	99
5.4012-49.37	0.2296	112	0.2521	2893	X-RAY DIFFRACTION	99

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	3.0224	-0.0506	0.0327	2.6838	-0.051	2.7206	0.0138	0.3214	0.282	-0.1184	-0.0032	-0.162	-0.0569	0.2191	-0.0555	0.1057	0.0042	0.0117	0.1972	0.0085	0.152	17.3682	-35.622	-40.8115
2	3.2976	-0.7519	-0.1756	2.6656	0.7844	5.8377	0.0115	0.0828	0.01	0.0122	0.07	0.1017	0.0272	0.0903	-0.0655	0.1235	0.0062	-0.0167	0.1267	0.0184	0.1195	1.9152	-32.7555	-53.3652
3	3.2439	0.1078	-0.6403	2.4491	0.2891	3.1392	0.0147	0.2119	0.1622	0.0697	0.0672	0.2553	-0.1462	-0.4829	-0.1352	0.0887	0.0162	0.0026	0.107	0.043	0.1778	-11.3943	-1.1341	-4.4571
4	3.0965	-0.0386	0.1114	2.1988	0.2126	2.6749	-0.0266	-0.0206	-0.2538	0.0006	0.0416	-0.1137	0.2036	0.1482	0.0298	0.0981	0.0118	-0.0062	0.1111	-0.0097	0.1545	9.7386	0.0437	-6.2052
5	2.3812	2.3509	-0.8444	7.4954	-0.2712	2.6566	0.2932	-1.3618	-0.1897	1.2995	-0.2194	-0.2779	0.3642	0.1916	0.2992	0.3702	-0.0136	-0.0109	0.3631	0.073	0.1961	9.1528	2.3713	11.9456
6	2.4509	0.365	0.5706	2.2937	0.064	4.3166	0.0475	-0.1761	-0.0386	0.1224	0.0591	0.0629	0.0848	0.1834	-0.0352	0.0899	0.0257	0.0191	0.0989	0.0065	0.1278	-6.3423	-3.367	6.9135
7	4.0791	0.3765	0.7471	2.1914	-0.2184	2.9963	0.1168	0.2926	-0.0196	-0.1358	-0.093	-0.1222	-0.0543	0.2475	-0.0288	0.1512	-0.0097	0.0134	0.1364	-0.0275	0.1101	-7.8053	0.0707	-45.7186
8	3.6164	-0.5086	-0.6335	3.7436	-0.0193	3.4293	-0.0724	-0.2771	0.1312	0.039	0.0951	0.1026	-0.0689	-0.1078	-0.0151	0.1093	0.0143	-0.0267	0.18	0.0143	0.1204	-20.1029	-5.2557	-44.5068
9	3.0201	1.7959	-1.3444	1.6801	-2.2362	3.9966	0.2158	-0.4937	0.6968	0.9986	-0.0286	1.0691	0.1682	-1.0226	-0.3611	0.4904	-0.083	0.1512	0.4947	-0.0577	0.2682	-17.4722	-5.5063	-29.126
10	3.1447	0.9567	-0.1181	2.9317	-0.531	4.8038	0.1001	-0.3177	0.045	0.1857	0.035	-0.0197	0.113	-0.0882	-0.0615	0.1425	0.0182	-0.0268	0.1324	-0.02	0.1086	-4.2682	-0.9975	-30.2303
11	3.9153	0.0952	-0.5026	2.0653	-0.0599	3.279	0.0258	-0.2326	-0.1046	0.0763	0.0912	0.0297	0.0093	0.0765	-0.0736	0.1039	0.0205	-0.0348	0.0909	-0.0284	0.1444	-0.2262	-35.5242	-0.1112
12	3.3394	0.2408	-0.0812	2.375	-0.7951	1.947	-0.0277	0.2008	-0.111	-0.1184	0.0505	0.0885	0.1586	-0.1281	-0.0301	0.1092	-0.0071	-0.0131	0.1292	-0.0129	0.164	-12.2561	-30.0682	-3.1614
13	1.5078	-0.2935	0.3068	2.7377	-1.0342	4.6587	0.1397	0.175	0.0379	-0.1655	-0.1109	-0.121	0.094	-0.0548	-0.0015	0.1084	-0.0121	-0.0015	0.1439	-0.0225	0.1539	3.6867	-35.2917	-13.539
14	3.3706	-0.5152	1.3194	1.8942	0.6153	2.4799	0.0682	0.0342	-0.1631	0.0432	-0.1022	0.1685	0.0208	-0.3102	0.0092	0.1276	0.0156	-0.0243	0.2359	0.0411	0.1726	-3.6781	-34.2332	-40.8751

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 37 through 159 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 160 through 224 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 9 through 36 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 37 through 141 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 142 through 159 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 160 through 227 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 9 through 55 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 56 through 141 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 142 through 164 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 165 through 222 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 9 through 55 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 56 through 159 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 160 through 227 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 9 through 36 )

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