PDB-6k1m: Engineered form of a putative cystathionine gamma-lyase

ID or keywords:

Entry

Database: PDB / ID: 6k1m

Title

Engineered 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-lyase activity / L-cysteine desulfhydrase activity /

transsulfuration /

pyridoxal phosphate binding
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.32 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 2.0	Nov 15, 2023	Group: Atomic model / Data collection / Database references Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1	Nov 22, 2023	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6k1m.cif.gz	578 KB	Display	PDBx/mmCIF format
PDB format	pdb6k1m.ent.gz	479.1 KB	Display	PDB format
PDBx/mmJSON format	6k1m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k1/6k1m ftp://data.pdbj.org/pub/pdb/validation_reports/k1/6k1m	HTTPS FTP

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Related structure data

Related structure data	6k1lC 6k1nC 6k1oC 2nmpS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4iy7-d 4iyo-d 4ixz-d 6k1l-d 5eig-2 3e6g-d 6cjb-d 4q31-2 6nba-d 6le4-1 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
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: Cystathionine gamma-lyase

B: Cystathionine gamma-lyase

C: Cystathionine gamma-lyase

D: Cystathionine gamma-lyase

hetero molecules

173 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)	154.530, 154.530, 223.040
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	D-739- HOH

#1: Protein	Cystathionine gamma-lyase / Mass: 43067.098 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 / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PYR / PYRUVIC ACID / Pyruvic acid Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₄O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 279 / 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: 4.68 Å³/Da / Density % sol: 73.72 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 28% (v/v) polyethylene glycol 400, 0.2 M Calcium, 0.1 mM Na Acetate pH 4.6, 5 mM cysteine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.32→73.01 Å / Num. obs: 133321 / % possible obs: 100 % / Redundancy: 20 % / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.32→2.38 Å / Num. unique obs: 9779

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2NMP

2nmp

Resolution: 2.32→66.913 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.04

	R_factor	Num. reflection	% reflection
R_free	0.1891	3904	1.51 %
R_work	0.1647	-	-
obs	0.1651	133250	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.32→66.913 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11490	0	0	279	11769

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11742
X-RAY DIFFRACTION	f_angle_d	0.971	15943
X-RAY DIFFRACTION	f_dihedral_angle_d	15.378	6987
X-RAY DIFFRACTION	f_chiral_restr	0.063	1822
X-RAY DIFFRACTION	f_plane_restr	0.006	2071

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 (%)
2.32-2.3483	0.3427	142	0.2872	9071	X-RAY DIFFRACTION	100
2.3483-2.3781	0.3346	140	0.2766	9118	X-RAY DIFFRACTION	100
2.3781-2.4094	0.2955	140	0.2671	9012	X-RAY DIFFRACTION	100
2.4094-2.4424	0.2852	142	0.2613	9086	X-RAY DIFFRACTION	100
2.4424-2.4773	0.3084	144	0.2545	9067	X-RAY DIFFRACTION	100
2.4773-2.5142	0.241	140	0.247	9016	X-RAY DIFFRACTION	100
2.5142-2.5535	0.273	140	0.2455	9098	X-RAY DIFFRACTION	100
2.5535-2.5954	0.3049	140	0.2602	9038	X-RAY DIFFRACTION	100
2.5954-2.6401	0.2833	138	0.2546	9115	X-RAY DIFFRACTION	100
2.6401-2.6882	0.2691	140	0.2298	9044	X-RAY DIFFRACTION	100
2.6882-2.7399	0.2793	138	0.2123	9146	X-RAY DIFFRACTION	100
2.7399-2.7958	0.2362	132	0.1857	9028	X-RAY DIFFRACTION	100
2.7958-2.8566	0.2148	138	0.1794	9173	X-RAY DIFFRACTION	100
2.8566-2.923	0.2163	136	0.182	8973	X-RAY DIFFRACTION	100
2.923-2.9961	0.2575	134	0.1744	9020	X-RAY DIFFRACTION	100
2.9961-3.0771	0.2172	142	0.1718	9151	X-RAY DIFFRACTION	100
3.0771-3.1677	0.1852	133	0.1736	9071	X-RAY DIFFRACTION	100
3.1677-3.2699	0.2013	146	0.1707	9087	X-RAY DIFFRACTION	100
3.2699-3.3868	0.2029	142	0.1636	9006	X-RAY DIFFRACTION	100
3.3868-3.5224	0.1889	140	0.1536	9074	X-RAY DIFFRACTION	100
3.5224-3.6827	0.1279	136	0.146	9084	X-RAY DIFFRACTION	100
3.6827-3.8768	0.1772	138	0.1418	9117	X-RAY DIFFRACTION	100
3.8768-4.1197	0.1847	148	0.1388	9015	X-RAY DIFFRACTION	100
4.1197-4.4377	0.1479	144	0.1259	9079	X-RAY DIFFRACTION	100
4.4377-4.8842	0.1254	140	0.1196	9029	X-RAY DIFFRACTION	100
4.8842-5.5906	0.1621	135	0.1403	9103	X-RAY DIFFRACTION	100
5.5906-7.0424	0.1818	134	0.1706	9077	X-RAY DIFFRACTION	100
7.0424-66.9413	0.1504	142	0.1487	9059	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	0.6656	-0.2922	-0.4887	0.8156	-0.2274	0.6473	0.0075	-0.0921	0.0696	0.0544	0.021	-0.0914	0.0245	0.3848	-0.0001	0.389	-0.034	-0.0199	0.3598	-0.0219	0.39	90.6951	23.4141	-2.89
2	0.9283	0.2547	-0.8611	0.7695	0.3114	1.2042	0.0049	0.0604	0.1281	0.0197	0.0483	0.2231	-0.1305	-0.1201	0.0001	0.3824	-0.052	-0.0474	0.2837	-0.0021	0.3855	89.3726	53.5845	-1.383
3	0.9382	0.3427	0.3179	0.5926	0.2207	0.7836	-0.0411	0.0651	0.0865	-0.06	0.0385	0.0732	-0.0582	0.1004	-0.0001	0.3805	-0.0542	-0.0282	0.2803	0.0094	0.3354	82.5277	44.0435	-13.0949
4	1.1806	-0.0065	0.4582	0.42	-0.7186	1.076	0.0204	-0.1726	0.3085	0.293	-0.0307	0.1887	-0.1105	-0.2229	0.0001	0.5161	0.0256	-0.0044	0.3402	-0.0309	0.5618	63.5114	50.9612	-11.6948
5	-0.0279	-0.0765	-0.0934	0.0644	0.2039	0.1632	-0.0127	-0.0914	0.1634	0.0659	-0.0596	0.1797	-0.1832	-0.1948	0.0001	0.4802	-0.0358	0.0086	0.4397	-0.0914	0.4755	63.9217	29.0651	17.4639
6	0.3096	-0.0875	0.1917	0.0383	0.149	0.385	0.186	0.0514	0.2877	-0.0209	-0.0455	-0.1418	-0.471	0.0808	0.0002	0.5205	-0.0142	0.0594	0.2978	-0.0186	0.4786	67.4212	40.418	8.7948
7	0.4007	0.4181	0.0412	1.0372	-0.0109	0.9499	0.0646	-0.0248	-0.101	0.1079	-0.0185	-0.0616	0.0455	0.2196	0.0001	0.4113	-0.0627	-0.0044	0.3563	-0.0481	0.3327	93.1367	44.1712	22.2996
8	0.6375	0.2036	-0.2077	0.9414	0.1713	0.6711	0.0561	-0.0553	0.0363	0.123	0.0816	0.0122	-0.0087	0.0326	-0	0.4278	-0.0392	-0.0049	0.3012	-0.0668	0.3398	83.0819	32.6886	25.0673
9	0.8786	0.5562	0.303	2.5308	0.5487	1.9265	0.0732	-0.022	-0.1017	0.0174	0.1395	-0.3591	0.2064	0.3996	-0.0008	0.3552	-0.0032	-0.0581	0.4456	-0.1131	0.385	98.1266	19.1065	27.6598
10	0.9484	-0.3705	-0.5345	0.631	-0.0312	0.2431	0.0776	0.1035	-0.0508	-0.1025	-0.0423	-0.0376	0.261	0.0094	-0.0006	0.4615	-0.0251	-0.0304	0.3022	-0.0276	0.358	82.5601	7.1678	3.4937
11	0.3526	-0.0477	0.1405	0.8923	-0.0856	0.3043	0.0136	-0.0267	0.0068	0.1258	-0.0107	0.0936	0.0605	-0.1068	-0	0.4466	-0.0926	0.0147	0.3104	-0.0339	0.3672	56.6738	-3.6545	5.6448
12	1.2983	0.2845	0.1847	0.4216	0.271	0.4387	0.0623	-0.1925	0.0606	0.2416	-0.0638	0.2369	0.1242	-0.1143	0.0002	0.6587	-0.1139	0.0011	0.3773	0.0044	0.4276	61.0475	-8.3494	17.1281
13	0.5776	0.1064	0.0172	1.0471	0.583	1.3012	0.0891	-0.0781	-0.0363	0.2001	-0.0868	0.1079	0.1641	-0.0793	-0	0.4671	-0.0816	0.0165	0.3086	-0.0094	0.3495	65.4448	5.5238	19.8108
14	0.0574	-0.234	0.0813	0.356	-0.1326	0.6291	0.1739	0.169	0.1109	0.0927	-0.1319	0.3918	-0.1785	-0.2403	0.0003	0.4723	-0.0701	0.1075	0.5284	-0.0432	0.5924	50.7192	17.4364	25.2378
15	0.2229	-0.0778	-0.3148	1.103	-0.7365	0.8917	0.1134	-0.0411	0.4364	0.1105	0.0772	0.634	0.1473	-0.355	-0.0018	0.4983	-0.1813	0.0365	0.502	-0.01	0.5779	50.6674	12.5991	24.7111
16	0.2956	-0.2347	0.0779	0.3092	0.4127	0.7641	-0.004	-0.0996	0.0413	0.0454	-0.0413	0.1867	0.0535	-0.2903	-0.0006	0.3726	-0.0293	-0.0212	0.3822	-0.0235	0.4571	56.8789	25.3923	-0.5448
17	0.4476	-0.2657	0.2835	0.4137	-0.5289	0.9186	-0.0373	0.0694	0.0418	0.064	0.0362	-0.0611	0.176	0.0373	0.0001	0.4729	-0.0583	-0.0347	0.3474	-0.0196	0.4039	59.1419	0.4416	-13.2459
18	0.2816	0.0375	-0.6487	1.1424	0.3133	1.1097	-0.027	0.1376	-0.0654	-0.0743	-0.038	-0.0846	0.1158	-0.1211	0.0001	0.4554	-0.0417	-0.0594	0.4409	-0.0215	0.3831	56.0211	6.4927	-24.0781
19	0.6336	0.1191	-0.1115	0.8812	0.0827	0.3603	0.0391	0.0024	-0.0008	-0.095	-0.0111	0.0099	-0.0941	-0	0.0001	0.3791	-0.0325	-0.0351	0.2757	-0.0006	0.3011	66.9517	15.9873	-20.1673
20	0.3262	0.488	0.2239	0.589	0.0561	0.332	-0.0976	-0.1399	-0.0692	-0.12	0.2233	-0.1195	-0.27	0.3271	-0.0003	0.4374	-0.0248	0.0122	0.3446	-0.051	0.3392	84.7638	9.1865	-24.1001
21	2.2387	-0.5463	0.8377	0.3186	0.1414	0.8306	0.1015	0.069	-0.2311	0.0932	0.1149	-0.0118	0.044	0.1376	-0.0002	0.4593	-0.0452	-0.0175	0.2778	-0.0258	0.3107	80.539	6.8367	-25.5726

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 73 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 74 through 152 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 153 through 307 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 308 through 390 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 9 through 39 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 40 through 72 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 73 through 152 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 153 through 277 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 278 through 390 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 9 through 73 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 74 through 130 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 131 through 203 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 204 through 307 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 308 through 341 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 342 through 390 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 9 through 72 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 73 through 130 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 131 through 203 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 204 through 307 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 308 through 341 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 342 through 390 )

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