PDB-6k1o: Apo form of a putative cystathionine gamma-lyase

ID or keywords:

Entry

Database: PDB / ID: 6k1o

Title

Apo 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: 2.033 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	6k1o.cif.gz	553.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6k1o.ent.gz	456.4 KB	Display	PDB format
PDBx/mmJSON format	6k1o.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6k1o_validation.pdf.gz	458.9 KB	Display	wwPDB validaton report
Full document	6k1o_full_validation.pdf.gz	474.3 KB	Display
Data in XML	6k1o_validation.xml.gz	56.3 KB	Display
Data in CIF	6k1o_validation.cif.gz	80.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k1/6k1o ftp://data.pdbj.org/pub/pdb/validation_reports/k1/6k1o	HTTPS FTP

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Related structure data

Related structure data	6k1lC 6k1mC 6k1nC 2nmpS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6kgz-1 4q31-1 5tsu-1 4ixs-1 6ovg-2 1n8p-d 4ixz-d 3e6g-d 5eig-2 6ldo-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

Deposited unit

A: Cystathionine gamma-lyase

B: Cystathionine gamma-lyase

C: Cystathionine gamma-lyase

D: Cystathionine gamma-lyase

167 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)	61.747, 154.303, 158.995
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: 41702.551 Da / Num. of mol.: 4 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.41 Å³/Da / Density % sol: 48.89 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% (v/v) polyethylene glycol 3350, 200 mM Calcium acetate, 100 mM Tris pH 7.0, 5 mM 3-cyano-L-alanine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 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: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.03→100 Å / Num. obs: 97813 / % possible obs: 99.5 % / Redundancy: 6.2 % / Net I/σ(I): 17.5
Reflection shell	Resolution: 2.03→2.07 Å / Redundancy: 4.7 % / R_merge(I) obs: 1.16 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4713 / CC_1/2: 0.618 / R_pim(I) all: 0.563 / R_rim(I) all: 1.295 / % possible all: 97.3

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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: 2.033→33.422 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.61

	R_factor	Num. reflection	% reflection
R_free	0.242	1994	2.05 %
R_work	0.1885	-	-
obs	0.1896	97492	98.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.033→33.422 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10883	0	0	575	11458

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11113
X-RAY DIFFRACTION	f_angle_d	1.063	15094
X-RAY DIFFRACTION	f_dihedral_angle_d	9.116	6625
X-RAY DIFFRACTION	f_chiral_restr	0.064	1778
X-RAY DIFFRACTION	f_plane_restr	0.007	1950

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 (%)
2.0325-2.0833	0.3024	134	0.284	6210	X-RAY DIFFRACTION	92
2.0833-2.1396	0.3474	137	0.2575	6790	X-RAY DIFFRACTION	99
2.1396-2.2026	0.3112	135	0.2471	6762	X-RAY DIFFRACTION	99
2.2026-2.2737	0.3642	147	0.2789	6794	X-RAY DIFFRACTION	100
2.2737-2.3549	0.2862	141	0.2178	6767	X-RAY DIFFRACTION	100
2.3549-2.4492	0.2731	142	0.2075	6837	X-RAY DIFFRACTION	100
2.4492-2.5606	0.284	142	0.2041	6821	X-RAY DIFFRACTION	100
2.5606-2.6955	0.2978	144	0.1984	6865	X-RAY DIFFRACTION	100
2.6955-2.8643	0.269	139	0.197	6814	X-RAY DIFFRACTION	100
2.8643-3.0854	0.2815	146	0.1966	6915	X-RAY DIFFRACTION	100
3.0854-3.3956	0.2366	144	0.1866	6887	X-RAY DIFFRACTION	100
3.3956-3.8863	0.2331	144	0.172	6970	X-RAY DIFFRACTION	100
3.8863-4.8939	0.1884	146	0.1436	6941	X-RAY DIFFRACTION	99
4.8939-33.4269	0.1802	153	0.1707	7125	X-RAY DIFFRACTION	98

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	0.2453	0.1743	0.1231	0.2337	-0.1503	0.2352	-0.0023	-0.0127	-0.0362	0.1698	0.0267	-0.0495	-0.0338	0.2982	-0	0.2104	-0.0412	-0.0305	0.3414	-0.0308	0.3016	36.9228	8.1206	-4.0147
2	0.281	0.0756	-0.0736	0.2858	0.0492	0.5987	0.0743	-0.0453	0.0727	0.0626	-0.0555	-0.0766	-0.258	0.1479	-0.0017	0.2708	-0.0977	-0.0084	0.256	-0.019	0.2518	34.9837	21.2619	-6.0502
3	0.1119	0.0252	0.0516	0.1196	0.0265	0.0266	0.0283	-0.1237	-0.0353	-0.0072	0.02	0.1473	-0.2628	-0.1921	0.0001	0.3442	0.0608	0.0589	0.3506	-0.0099	0.3175	16.0582	26.0135	-13.1083
4	0.0284	0.0054	0.0018	0.0154	0.0005	0.0047	0.0282	-0.012	0.1502	0.0333	0.0226	0.0528	0.0781	-0.121	-0.0001	0.3291	-0.0206	0.0137	0.2828	0.0194	0.3447	13.1586	-4.1667	-13.7319
5	0.0059	0.0307	-0.0079	0.0291	-0.0514	0.0516	0.0238	0.0219	0.0431	0.1234	0.0203	-0.0046	0.2156	0.081	-0.0002	0.2558	0.0142	-0.057	0.2363	-0.0212	0.2483	26.7341	-5.736	7.8155
6	0.1262	0.1783	0.1439	0.2609	0.1953	0.6573	0.0329	-0.0303	-0.0179	0.0497	0.0738	-0.0226	0.2061	0.1488	0.0015	0.3158	0.0572	-0.034	0.1826	-0.0131	0.1966	26.3535	-19.3836	5.2222
7	0.0843	-0.0156	0.0461	0.0528	-0.0383	0.0357	0.0539	0.0098	0.0114	0.0335	0.0254	0.0535	-0.0371	0.7183	0.0014	0.4569	0.0267	-0.0419	0.5854	-0.0865	0.2898	40.9928	-26.0154	-1.0255
8	0.0079	-0.0087	0.0057	0.0067	-0.0059	0.0025	-0.0917	0.0121	0.0488	-0.0113	-0.021	-0.0861	-0.0874	0.1527	0	0.4867	0.097	-0.0641	0.3929	-0.0242	0.3961	38.7433	-24.1201	-18.7825
9	-0.0087	-0.0001	0.0005	0.0642	-0.0199	0.0514	0.0418	0.0993	0.0068	-0.0507	0.0156	-0.0941	0.0618	0.1723	-0	0.2778	0.0784	0.0081	0.287	-0.0512	0.2659	34.6176	-15.5875	-31.7786
10	0.023	-0.0197	0.0175	0.0318	0.0049	0.0157	0.0249	0.1611	0.0026	0.0871	0.02	0.2696	0.2506	0.0124	0.0002	0.4916	0.0124	0.0278	0.3015	-0.0049	0.3363	18.0052	-20.9429	-50.6573
11	0.066	-0.009	0.0174	0.0804	-0.0195	0.0582	0.067	0.0269	-0.0249	-0.0712	0.0564	-0.0542	0.3164	-0.0194	0	0.4647	0.0482	-0.006	0.291	-0.0563	0.2974	22.0204	-32.4236	-42.1696
12	0.0584	-0.0585	0.1296	0.1352	-0.0984	0.4196	0.0327	-0.0053	-0.0413	0.065	-0.0166	-0.0415	0.2873	0.0077	0	0.3291	0.005	0.0046	0.2044	-0.0289	0.2366	20.0263	-26.3328	-28.6589
13	0.0876	0.0514	-0.007	0.0957	0.0149	0.0339	0.0128	0.1551	0.0762	-0.0613	-0.0222	0.0803	-0.0323	-0.2736	-0.0002	0.3355	-0.0113	-0.074	0.3827	0.0324	0.3149	2.0633	-22.6385	-27.5624
14	0.1004	0.0602	0.0957	0.0994	-0.0274	0.1527	0.0275	0.0779	-0.0338	0.0629	-0	0.0814	-0.0029	-0.0675	-0	0.2036	0.0187	0.0348	0.2119	0.0018	0.2314	19.208	3.6845	-33.0916
15	0.018	-0.0376	-0.0111	0.0542	0.0031	0.0154	0.013	0.0922	0.0325	-0.0935	-0.1054	-0.1341	0.0353	0.2826	-0.0007	0.2723	0.0075	0.0368	0.3865	0.0049	0.3268	34.8768	-5.1215	-55.7287
16	0.099	-0.0262	0.0039	0.0981	0.0088	0.0331	0.0954	0.0686	0.0523	-0.2781	-0.0103	-0.0396	-0.3849	0.173	0.0006	0.3177	-0.0741	0.0743	0.3485	-0.0162	0.2704	31.1526	9.2	-54.1747
17	0.1108	0.0601	0.1061	0.0332	0.0203	0.4508	-0.0011	0.1642	-0.0655	-0.104	0.141	0.0512	-0.3245	0.3412	0.0111	0.235	-0.1257	0.0708	0.3268	-0.0319	0.1956	35.0424	10.6896	-39.6891
18	0.1129	-0.0412	-0.0552	0.0234	0.0258	0.1362	-0.0064	0.1084	-0.2582	-0.135	0.1279	-0.1097	0.014	0.747	0.2793	-0.1012	-0.2613	0.3675	0.926	-0.1729	0.3287	52.7075	7.5098	-39.3374

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 130 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 131 through 307 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 308 through 390 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 10 through 59 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 60 through 130 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 131 through 325 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 326 through 390 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 9 through 29 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 30 through 94 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 95 through 130 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 131 through 203 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 204 through 307 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 308 through 390 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 9 through 94 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 95 through 130 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 131 through 203 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 204 through 307 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 308 through 390 )

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