PDB-6k1l: E53A mutant of a putative cystathionine gamma-lyase

ID or keywords:

Entry

Database: PDB / ID: 6k1l

Title

E53A mutant 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: 2.46 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	6k1l.cif.gz	563.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6k1l.ent.gz	465.3 KB	Display	PDB format
PDBx/mmJSON format	6k1l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6k1l_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	6k1l_full_validation.pdf.gz	1.8 MB	Display
Data in XML	6k1l_validation.xml.gz	57.5 KB	Display
Data in CIF	6k1l_validation.cif.gz	78.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k1/6k1l ftp://data.pdbj.org/pub/pdb/validation_reports/k1/6k1l	HTTPS FTP

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Related structure data

Related structure data	6k1mC 6k1nC 6k1oC 2nmpS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4iyo-d 4iy7-d 4ixs-1 6k1m-d 6cjb-d 5eig-2 4ixz-d 6nba-d 6cja-d 6ovg-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
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

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)	59.970, 148.460, 156.970
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: 41644.516 Da / Num. of mol.: 4 / Mutation: E53A 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: Chemical	ChemComp-PYR / 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 Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.15 Å³/Da / Density % sol: 42.73 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium sulphate, 20% (v/v) polyethylene glycol 3350, 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: 2.46→74.23 Å / Num. obs: 51467 / % possible obs: 99.3 % / Redundancy: 12.3 % / Net I/σ(I): 11.4
Reflection shell	Resolution: 2.46→2.52 Å / Num. unique obs: 3612

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2NMP

2nmp

Resolution: 2.46→67.105 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.73

	R_factor	Num. reflection	% reflection
R_free	0.2757	3771	3.87 %
R_work	0.2057	-	-
obs	0.2084	51396	99.17 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.46→67.105 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11470	0	0	212	11682

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11733
X-RAY DIFFRACTION	f_angle_d	1.004	15927
X-RAY DIFFRACTION	f_dihedral_angle_d	15.912	6980
X-RAY DIFFRACTION	f_chiral_restr	0.059	1824
X-RAY DIFFRACTION	f_plane_restr	0.007	2066

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 (%)
2.46-2.4912	0.5383	152	0.5157	3307	X-RAY DIFFRACTION	94
2.4912-2.5239	0.5342	147	0.5147	3344	X-RAY DIFFRACTION	98
2.5239-2.5585	0.5793	136	0.4637	3473	X-RAY DIFFRACTION	100
2.5585-2.5951	0.4636	131	0.4365	3531	X-RAY DIFFRACTION	100
2.5951-2.6338	0.3995	146	0.4058	3487	X-RAY DIFFRACTION	100
2.6338-2.675	0.5549	131	0.4242	3475	X-RAY DIFFRACTION	100
2.675-2.7188	0.4438	126	0.3616	3527	X-RAY DIFFRACTION	100
2.7188-2.7657	0.3946	149	0.3079	3439	X-RAY DIFFRACTION	99
2.7657-2.816	0.3889	155	0.3246	3472	X-RAY DIFFRACTION	100
2.816-2.8702	0.3747	114	0.2941	3583	X-RAY DIFFRACTION	100
2.8702-2.9288	0.3207	144	0.2699	3413	X-RAY DIFFRACTION	100
2.9288-2.9924	0.3346	146	0.2421	3537	X-RAY DIFFRACTION	100
2.9924-3.062	0.2751	131	0.1932	3430	X-RAY DIFFRACTION	100
3.062-3.1386	0.2959	139	0.1765	3547	X-RAY DIFFRACTION	100
3.1386-3.2235	0.2862	148	0.1651	3468	X-RAY DIFFRACTION	100
3.2235-3.3183	0.2435	132	0.1609	3495	X-RAY DIFFRACTION	100
3.3183-3.4254	0.2245	120	0.1607	3512	X-RAY DIFFRACTION	100
3.4254-3.5479	0.2721	151	0.1616	3522	X-RAY DIFFRACTION	100
3.5479-3.6899	0.2111	133	0.1463	3295	X-RAY DIFFRACTION	95
3.6899-3.8578	0.2049	147	0.139	3516	X-RAY DIFFRACTION	100
3.8578-4.0612	0.225	140	0.1389	3496	X-RAY DIFFRACTION	100
4.0612-4.3156	0.1812	149	0.1238	3528	X-RAY DIFFRACTION	100
4.3156-4.6487	0.157	142	0.1149	3479	X-RAY DIFFRACTION	100
4.6487-5.1164	0.2009	137	0.1241	3474	X-RAY DIFFRACTION	100
5.1164-5.8564	0.221	134	0.1572	3522	X-RAY DIFFRACTION	100
5.8564-7.3769	0.2008	143	0.1768	3389	X-RAY DIFFRACTION	97
7.3769-67.1299	0.2035	148	0.1586	3472	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	0.067	0.0455	-0.0382	0.018	-0.0211	0.011	-0.0412	0.0249	0.0244	0.0142	-0.0632	-0.1796	-0.1082	0.0729	0	0.0934	0.0104	-0.0193	0.1212	-0.0023	0.1501	10.4946	14.4791	-52.1826
2	0.0304	-0.0384	0.0038	0.2488	-0.0173	0.0205	-0.0464	-0.017	0.0655	0.0512	0.0452	0.3409	-0.1277	0.0482	-0.0007	0.2119	0.0417	-0.0142	0.1277	-0.0092	0.1344	-7.8866	23.171	-30.2331
3	0.1538	0.0487	-0.1102	0.1102	-0.1266	0.1116	-0.0119	0.0579	0.0206	0.0372	-0.0324	-0.0147	0.0148	0.022	-0.0035	0.0946	0.0132	-0.0131	0.0451	-0.0192	0.0713	-5.6384	25.4662	-45.5778
4	0.1327	0.0012	0.0485	0.0205	-0.0208	0.1048	-0.0669	-0.018	0.1417	0.1877	-0.1834	0.3537	-0.0258	-0.308	-0.0848	0.2009	-0.0152	0.095	0.1921	-0.0882	0.2094	-25.6316	26.3954	-49.2134
5	2	-5.6705	2	2	3.846	2	0.6656	0.1408	0.0369	-0.5774	-0.0896	-0.4509	-0.2457	0.6382	-0.578	0.7959	-0.0128	0.1531	0.6435	-0.0095	0.8489	-17.132	21.615	-54.6
6	0.0192	0.0214	-0.0111	0.0204	-0.0169	0.0049	0.0423	0.0762	-0.028	0.0109	0.0125	0.198	0.0413	-0.0335	-0.0001	0.12	0.0061	0.0146	0.1357	0.008	0.1574	-15.045	-3.2243	-48.8105
7	0.0096	0.0456	-0.0084	0.1064	0.0271	0.041	-0.0077	-0.0411	-0.0318	-0.0134	-0.0058	-0.0073	-0.0155	-0.0106	0	0.0723	0.0125	0.0083	0.0926	0.0117	0.0905	-0.6449	-3.6147	-28.4265
8	0.3044	0.2464	-0.0697	0.2571	-0.0726	0.1219	-0.1348	0.0183	-0.3354	-0.0407	0.0159	-0.1779	-0.09	0.0757	-0.0654	0.1043	0.002	-0.0047	0.0916	-0.0117	0.0239	10.7663	-17.1045	-39.3883
9	0.043	-0.0488	0.0326	0.0364	-0.0203	0.0636	-0.0118	0.0049	-0.0182	-0.0296	-0.0733	-0.0881	-0.0503	0.037	-0.0005	0.1264	-0.0196	-0.0383	0.129	0.0079	0.1465	21.8398	-7.8045	-39.2043
10	0.0101	0.0027	-0.0123	0.0308	-0.0014	0.0225	-0.0286	0.0478	0.0475	0.0202	-0.0713	-0.0595	0.0941	-0.0584	0.0005	0.1518	0.006	-0.0175	0.1305	0.0065	0.1288	15.0374	-3.8716	-58.2839
11	0.0288	-0.0122	0.016	0.0195	0.0168	0.018	-0.0466	0.05	0.0454	0.0438	-0.0696	-0.0551	0.0548	0.0091	-0.0006	0.137	0.014	-0.0068	0.1493	0.0058	0.1308	13.4216	3.9694	-69.8343
12	0.0215	-0.0195	-0.0001	0.007	-0.0035	0.0093	-0.0339	-0.0261	-0.1469	-0.0183	0.0404	0.0384	0.1228	0.0805	0	0.1352	0.0278	0.0097	0.1222	-0.009	0.1406	0.3028	-13.1273	-84.8158
13	0.0317	0.0089	0.0134	0.0293	0.0348	0.0159	0.0164	0.0932	-0.1999	0.0036	-0.0189	0.05	0.0265	-0.0514	0	0.1924	0.017	0.0111	0.1357	-0.0026	0.1446	7.0538	-23.433	-80.6403
14	0.0842	0.0086	0.0987	0.0641	-0.0683	0.1122	-0.0136	0.0527	-0.0111	-0.0021	-0.0201	0.0192	0.0052	0.0238	-0	0.0947	0.0038	0.0166	0.0629	-0.005	0.1031	2.375	-19.4915	-67.1764
15	0.0244	0.0046	-0.0255	0.0085	-0.015	0.0365	-0.0722	0.0331	-0.0572	0.0219	-0.0971	0.0515	-0.0851	0.0192	-0.003	0.1601	-0.005	-0.0154	0.0901	-0.0254	0.1987	-16.0107	-24.7181	-63.6682
16	-0.002	-0.0174	0.0004	0.0146	0.0051	0.001	0.0158	0.035	0.0661	-0.1233	-0.1147	0.1633	-0.0447	-0.0939	-0.095	0.1078	-0.1271	-0.2078	-0.0976	-0.2616	-0.218	-13.3526	-26.0384	-67.5106
17	0.0782	0.0312	0.0045	0.0057	0.0026	0.045	0.0262	0.0506	-0.0691	-0.0973	0.1143	0.2374	0.032	-0.076	0.0034	0.1211	-0.0251	-0.011	0.1237	0.0154	0.1599	-17.0021	2.725	-66.964
18	0.0475	-0.0142	0.0234	0.0001	0.001	0.0323	-0.0398	0.0675	0.0547	0.0101	0.0175	-0.0097	-0.0303	0.0181	0	0.1117	-0.0135	-0.0121	0.1284	-0.0012	0.1203	-1.8363	7.9407	-92.3287
19	0.0377	0.022	0.0116	0.0971	0.0546	0.1222	-0.0602	0.019	0.0193	0.0692	-0.007	-0.0165	0.0326	-0.0777	-0.5128	-0.0142	0.0066	-0.0292	0.0326	0.0087	0.0245	-5.9507	18.771	-81.0805
20	0.1732	0.042	0.2005	0.1281	0.0237	0.2231	-0.009	0.2057	0.0231	0.0292	0.0663	-0.1152	0.0796	0.0917	0.0361	0.0802	0.0015	0.0162	0.1051	0.0429	0.0857	12.0829	25.7252	-77.9019

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 277 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 278 through 390 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 701 through 701 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 9 through 73 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 74 through 243 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 244 through 307 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 308 through 390 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 9 through 39 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 40 through 73 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 74 through 130 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 131 through 203 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 204 through 307 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 308 through 341 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 342 through 390 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 9 through 73 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 74 through 152 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 153 through 307 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 308 through 390 )

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