PDB-6k1n: PLP-bound form of a putative cystathionine gamma-lyase

ID or keywords:

Entry

Database: PDB / ID: 6k1n

Title

PLP-bound form of a putative cystathionine gamma-lyase

Components

Cystathionine gamma-lyase

Keywords

LYASE / CSE / CGL / biomineralization / quantum dots / CdS / BIOSYNTHETIC PROTEIN

Function / homology

Function and homology information

cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.26 Å

Authors

Chen, S. / Wang, Y.

Funding support

China, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2021
Title: Structural characterization of cystathionine gamma-lyase smCSE enables aqueous metal quantum dot biosynthesis.
Authors: Wang, Y. / Chen, H. / Huang, Z. / Yang, M. / Yu, H. / Peng, M. / Yang, Z. / Chen, S.

History

Deposition	May 10, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 13, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 2, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6k1n.cif.gz	558.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6k1n.ent.gz	462.1 KB	Display	PDB format
PDBx/mmJSON format	6k1n.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6k1n_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	6k1n_full_validation.pdf.gz	1.6 MB	Display
Data in XML	6k1n_validation.xml.gz	55.1 KB	Display
Data in CIF	6k1n_validation.cif.gz	77.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k1/6k1n ftp://data.pdbj.org/pub/pdb/validation_reports/k1/6k1n	HTTPS FTP

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Related structure data

Related structure data	6k1lC 6k1mC 6k1oC 2nmpS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1cs1-d 4iy7-d 2nmp-d 4ixs-1 4iyo-d 6k1m-d 6nba-d 6cjb-d 4ixz-d 5eig-2 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: Cystathionine gamma-lyase

B: Cystathionine gamma-lyase

C: Cystathionine gamma-lyase

D: Cystathionine gamma-lyase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	90.025, 141.735, 157.833
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Cystathionine gamma-lyase Mass: 41770.629 Da / Num. of mol.: 4 / Mutation: D223E, E276D, A290P, K300R, D318E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain R551-3) (bacteria) Strain: R551-3 / Gene: Smal_0489 / Production host: Escherichia coli (E. coli) / References: UniProt: B4SII9, cystathionine gamma-lyase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 418 / 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: 3 Å³/Da / Density % sol: 58.96 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 26% (v/v) polyethylene glycol 400, 0.2 M Calcium, 0.1 mM Na Acetate pH 4.2, 2 mM PLP

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.25→157.83 Å / Num. obs: 93522 / % possible obs: 97.5 % / Redundancy: 6.7 % / Net I/σ(I): 5.6
Reflection shell	Resolution: 2.25→2.29 Å / Num. unique obs: 2374

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
DIALS		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2NMP

2nmp

Resolution: 2.26→105.455 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2423	2000	2.15 %
R_work	0.1884	-	-
obs	0.1896	92917	97.69 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.26→105.455 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11181	0	0	418	11599

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11508
X-RAY DIFFRACTION	f_angle_d	1.038	15630
X-RAY DIFFRACTION	f_dihedral_angle_d	8.471	9340
X-RAY DIFFRACTION	f_chiral_restr	0.063	1802
X-RAY DIFFRACTION	f_plane_restr	0.007	2022

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	0.0905	0.1104	-0.0136	0.4149	-0.24	0.2821	0.0713	-0.0513	0.0072	0.1885	-0.0535	-0.0331	-0.0886	0.0531	-0	0.2086	-0.0472	-0.006	0.207	-0.0096	0.172	44.33	12.9986	-9.6749
2	0.6696	0.3452	0.3818	0.2114	0.3631	0.6579	-0.0598	-0.1556	0.0989	-0.0013	-0.0746	0.1354	-0.105	-0.1292	-0.0001	0.2275	0.0027	0.0442	0.2072	-0.0381	0.2131	29.1011	26.4073	-21.2053
3	0.1249	0.0311	-0.1106	0.0471	-0.0063	0.0323	0.0456	-0.0284	0.1721	0.1951	0.0147	0.1523	-0.1916	-0.1915	-0	0.2126	0.0662	0.0142	0.2679	-0.0177	0.3071	19.7361	-1.5189	-20.7618
4	0.1824	0.1432	-0.1888	0.2411	-0.0216	0.1445	-0.0021	0.0003	-0.0637	0.0845	0.0043	-0.0394	-0.1105	0.1301	0	0.1569	0.0176	0.0091	0.1507	-0.0015	0.135	34.5588	-8.2572	2.9705
5	0.1614	0.0364	-0.2853	0.1249	0.3091	0.8292	-0.0193	-0.0081	-0.0197	0.0245	0.0075	0.0237	0.1228	0.0374	-0	0.1519	0.0177	0.0079	0.1433	0.0006	0.1557	32.2845	-19.3278	-5.0536
6	0.4115	0.0594	-0.302	0.1997	-0.0749	0.2003	-0.1469	-0.2261	0.1	0.0105	0.1019	-0.0335	0.0355	0.1939	0.0004	0.1822	0.0943	-0.0245	0.2834	-0.0333	0.2055	50.6998	-26.2224	-8.8775
7	0.1492	-0.045	-0.134	0.0386	0.0965	0.1327	-0.0658	0.0456	0.0062	-0.1746	0.0879	-0.1337	-0.0149	0.0708	-0	0.1734	0.0013	0.0154	0.2113	-0.0238	0.2087	46.1567	-16.2285	-32.9299
8	0.0324	-0.1048	0.0001	0.1333	-0.0118	0.0827	-0.0344	0.0242	0.0515	-0.0252	-0.0034	0.099	0.0977	0.0402	0.0002	0.2373	-0.0043	-0.0034	0.1914	-0.0046	0.2189	29.2154	-18.5566	-53.8098
9	0.1643	0.1246	0.0174	0.2781	-0.2099	0.2412	-0.003	0.0148	0.0159	-0.1264	0.0237	0.0428	-0.0452	0.0222	0	0.1909	0.0252	-0.0223	0.1576	-0.0133	0.1743	30.0171	-28.5155	-49.0091
10	0.0091	0.0059	-0.0239	0.0491	-0.0239	0.0363	-0.0249	-0.0405	0.151	-0.0688	0.0309	0.1241	-0.3279	-0.0401	0.0004	0.1993	-0.0093	0.0583	0.218	-0.0043	0.1676	43.3128	-15.3065	-50.1408
11	0.1522	-0.1549	0.0712	0.1483	0.0519	0.1327	0.036	-0.0048	0.0236	0.0625	-0.0571	0.1094	-0.0591	-0.013	-0.0001	0.1077	0.0004	-0.0018	0.1207	-0.0188	0.1681	21.7724	-30.9763	-33.1177
12	0.0624	0.0442	0.027	0.0998	-0.139	0.4505	0.0872	0.1087	0.1095	-0.0243	-0.2274	0.2866	-0.214	0.0774	-0.0047	0.0839	0.0704	-0.038	0.2605	-0.0744	0.3597	8.9713	-21.3353	-33.6139
13	0.0487	-0.0112	0.0556	0.0015	-0.0085	0.1318	0.0324	0.3377	0.0451	-0.4827	-0.0004	0.2215	-0.0164	-0.2228	0.0044	0.5126	0.1191	-0.0662	0.5508	0.0013	0.4119	10.3562	-20.83	-47.2461
14	0.0553	-0.0378	-0.0333	0.0527	0.0361	0.0145	0.0124	0.0107	-0.1766	0.0447	-0.2247	0.0641	0.1021	-0.0782	-0.0001	0.092	-0.0007	-0.0103	0.2311	-0.0761	0.2755	10.4292	-25.6493	-29.7728
15	0.1593	0.0381	-0.0321	0.0533	0.0237	-0.0202	-0.0317	-0.0523	-0.1003	0.0459	0.0281	0.0644	0.0263	-0.0883	-0	0.1918	0.0109	0.0035	0.2206	0.0029	0.2087	23.3471	5.7114	-36.7521
16	0.1101	0.0288	0.1727	0.1725	-0.0957	0.3043	0.0292	0.0187	0.101	0.0618	-0.0844	-0.1142	0.2215	0.0939	0	0.2636	0.0452	-0.0038	0.1877	0.0089	0.204	38.7424	-2.299	-59.5912
17	0.1012	0.0833	0.0759	0.095	-0.0323	0.1224	0.017	0.0066	-0.0237	-0.0231	-0.016	-0.0375	-0.0499	-0.0004	-0	0.1648	-0.005	-0.0158	0.1663	-0.0002	0.167	35.4524	7.5087	-57.0808
18	0.3	0.1803	0.2198	0.2501	0.2595	0.3566	-0.0204	0.044	0.0226	0.0091	0.0237	-0.0431	-0.0958	0.0713	-0	0.1382	-0.0044	0.0112	0.1627	0.0245	0.1673	51.8322	16.3085	-47.2657
19	0.2926	-0.1005	-0.0575	0.1194	-0.0382	0.0439	0.0068	0.1066	-0.1214	0.0185	-0.0329	-0.0066	0.0786	-0.0075	-0.0001	0.1942	-0.0038	-0.0077	0.1951	-0.0165	0.1764	57.9311	8.9996	-47.0587

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 243 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 244 through 390 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 10 through 59 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 60 through 152 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 153 through 307 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 308 through 390 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 9 through 73 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 74 through 123 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 124 through 224 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 225 through 243 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 244 through 307 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 308 through 341 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 342 through 362 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 363 through 390 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 8 through 73 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 74 through 130 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 131 through 243 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 244 through 326 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 327 through 390 )

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