PDB-6nba: Crystal structure of Human Cystathionine gamma lyase with S-3-Car...

ID or keywords:

Entry

Database: PDB / ID: 6nba

Title

Crystal structure of Human Cystathionine gamma lyase with S-3-Carboxpropyl-L-Cysteine

Components

Cystathionine gamma-lyase

Keywords

LYASE /

complex

Function / homology

Function and homology information

protein sulfhydration / selenocystathionine gamma-lyase activity / positive regulation of aortic smooth muscle cell differentiation / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine /

homocysteine desulfhydrase /

homocysteine desulfhydrase activity / Cysteine formation from homocysteine / Degradation of cysteine and homocysteine /

cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.495 Å

Authors

Kim, H. / Yadav, P.K. / Banerjee, R. / Cho, U.-S.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2019
Title: S-3-Carboxypropyl-l-cysteine specifically inhibits cystathionine gamma-lyase-dependent hydrogen sulfide synthesis.
Authors: Yadav, P.K. / Vitvitsky, V. / Kim, H. / White, A. / Cho, U.S. / Banerjee, R.

History

Deposition	Dec 6, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jul 24, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 11, 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	6nba.cif.gz	603.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6nba.ent.gz	503.9 KB	Display	PDB format
PDBx/mmJSON format	6nba.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	2nmpS S: Starting model for refinement
Similar structure data	5eig-2 4iy7-d 4iyo-d 6ovg-2 6k1m-d 6ovg-1 6cjb-d 4ixz-d 5tsu-1 6k1l-d 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

178 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)	68.551, 152.167, 83.771
Angle α, β, γ (deg.)	90.00, 112.25, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cystathionine gamma-lyase / / Cysteine-protein sulfhydrase / Gamma-cystathionase Mass: 44248.590 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTH / Production host: Escherichia coli (E. coli) / References: UniProt: P32929, cystathionine gamma-lyase
#2: Chemical	ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID Mass: 318.220 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.35 Å³/Da / Density % sol: 47.77 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.03 M sodium nitrate 0.03 M sodium phosphate dibasic 0.03 M ammonium sulfate 12.5% (v/v) Methyl-2,4-pentanediol (MPD) 12.5% (v/v) PEG 1000 12.5% (w/v) PEG 3350 0.1 M Tris-BICINE buffer (pH 8.5)

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.495→50 Å / Num. obs: 54611 / % possible obs: 99.2 % / Redundancy: 4.2 % / R_merge(I) obs: 0.125 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.5→2.56 Å / R_merge(I) obs: 0.61 / Num. unique all: 5155

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3211: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2NMP

2nmp

Resolution: 2.495→42.446 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.02

	R_factor	Num. reflection	% reflection
R_free	0.2303	2008	3.68 %
R_work	0.1957	-	-
obs	0.1969	54556	98.82 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.495→42.446 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12051	0	84	194	12329

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	12408
X-RAY DIFFRACTION	f_angle_d	0.838	16840
X-RAY DIFFRACTION	f_dihedral_angle_d	6.363	7420
X-RAY DIFFRACTION	f_chiral_restr	0.06	1909
X-RAY DIFFRACTION	f_plane_restr	0.007	2162

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 (%)
2.495-2.5574	0.3516	129	0.3124	3356	X-RAY DIFFRACTION	89
2.5574-2.6266	0.3524	138	0.2973	3669	X-RAY DIFFRACTION	97
2.6266-2.7039	0.3026	144	0.2695	3747	X-RAY DIFFRACTION	99
2.7039-2.7911	0.3256	151	0.2628	3788	X-RAY DIFFRACTION	100
2.7911-2.8908	0.2737	141	0.2565	3776	X-RAY DIFFRACTION	100
2.8908-3.0066	0.2933	147	0.2393	3787	X-RAY DIFFRACTION	100
3.0066-3.1434	0.275	140	0.2317	3780	X-RAY DIFFRACTION	100
3.1434-3.309	0.2684	145	0.2223	3783	X-RAY DIFFRACTION	100
3.309-3.5162	0.2592	152	0.1978	3791	X-RAY DIFFRACTION	100
3.5162-3.7876	0.2262	142	0.1856	3811	X-RAY DIFFRACTION	100
3.7876-4.1684	0.1891	146	0.1575	3793	X-RAY DIFFRACTION	100
4.1684-4.7709	0.1675	146	0.1437	3796	X-RAY DIFFRACTION	100
4.7709-6.0081	0.1801	144	0.1593	3832	X-RAY DIFFRACTION	100
6.0081-42.4522	0.1788	143	0.1604	3839	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	2.1348	-0.4698	0.3445	2.1932	0.1401	1.1384	0.1511	0.0674	-0.0139	0.0903	-0.0651	0.7245	0.1913	-0.3378	0.0059	0.3436	-0.0947	0.0373	0.353	-0.0012	0.4762	-1.5296	-2.2461	31.9207
2	0.8189	-0.6235	0.2578	1.3938	0.2926	1.3783	-0.2499	-0.2625	-0.0318	0.1625	0.2517	1.003	-0.3401	-0.5244	0.0192	0.3048	0.0369	0.0743	0.5175	0.0137	0.5808	-4.8611	6.2746	39.7046
3	0.7771	-0.2458	0.3305	1.5008	-0.5351	1.3979	-0.1345	-0.1157	0.0001	0.8733	0.0078	0.0021	0.0123	0.0816	0.0275	0.7173	0.0252	-0.0295	0.3172	-0.0108	0.2752	14.7178	1.2938	57.7684
4	2.1117	-0.3338	0.8242	2.3402	0.0142	1.4171	-0.0667	-0.3157	-0.0397	0.5002	-0.0028	0.1913	0.1755	0.0651	0.0873	0.5701	0.0107	-0.0069	0.2943	-0.0246	0.238	14.1493	-8.933	51.2789
5	0.8961	-0.2149	0.0636	2.4251	0.2477	1.1475	-0.0454	-0.1474	-0.1514	0.2461	0.0612	-0.0386	0.1556	0.1426	-0.0286	0.3744	0.0022	-0.0387	0.2214	0.0361	0.1898	17.0023	-5.1388	40.2057
6	0.9469	0.2686	-0.0747	1.8085	-0.44	1.8228	-0.0511	-0.0389	0.0913	0.1917	-0.0121	-0.5393	-0.1062	0.3734	0.0284	0.3669	0.0158	-0.109	0.4032	-0.0004	0.4389	34.7654	0.2451	39.023
7	0.7819	0.0573	0.0001	1.9466	-0.0006	1.0093	-0.0486	-0.1686	0.0842	0.6395	0.0138	0.2416	-0.3808	-0.0293	0.0431	0.6733	0.0421	0.015	0.297	-0.0286	0.2826	8.796	28.0364	48.2767
8	1.2448	-0.374	0.5151	1.5727	0.0703	1.3746	0.0295	-0.2715	0.0506	0.4133	0.0109	0.5936	-0.1584	-0.4301	-0.052	0.5493	0.029	0.1087	0.378	0.0181	0.5047	-8.612	29.5527	41.892
9	0.6412	0.0531	-0.1743	1.7118	-0.1151	1.1067	-0.0077	0.148	-0.0555	-0.2608	0.1011	0.7282	0.0925	-0.3115	-0.1158	0.3654	-0.0486	-0.1454	0.3741	0.0418	0.5693	-7.8361	16.3092	15.6396
10	0.926	0.7497	-0.1255	0.6647	0.0869	1.7669	-0.0348	0.1075	0.1515	-0.9996	-0.1242	0.2167	-0.2816	-0.0776	0.0877	0.9436	-0.067	-0.2223	0.4354	0.0826	0.4315	2.8768	28.1444	-8.9878
11	2.2268	-0.2448	-1.1193	0.1971	0.1918	1.4669	0.0081	0.5423	0.0001	-0.6336	0.0883	0.6313	-0.21	-0.3653	-0.0865	0.8097	-0.0361	-0.3286	0.4184	0.0812	0.531	-5.1591	33.384	1.3501
12	0.1387	0.35	-0.0102	1.8888	0.0339	1.0738	-0.1263	0.0935	0.0876	-0.296	0.0923	0.4492	-0.2397	-0.0738	0.0455	0.4877	-0.0115	-0.1465	0.2983	0.0266	0.3682	-0.4216	26.4553	13.7237
13	1.4679	0.5137	0.2773	1.9431	0.141	1.5023	-0.1113	0.1963	0.1041	-0.5065	0.1644	0.0992	-0.2945	0.1597	-0.0888	0.7308	-0.0801	-0.0317	0.2831	0.0401	0.277	13.5098	43.2558	10.1454
14	0.5292	0.0624	0.5477	3.1419	-0.1441	1.0598	0.1594	0.0824	-0.0011	-0.3445	-0.1302	-0.3478	-0.0946	0.2035	-0.0065	0.3118	-0.0213	0.0349	0.3556	0.0143	0.2939	24.171	8.0458	19.7946
15	0.5759	0.2106	0.441	4.576	0.3276	1.4062	-0.0539	-0.0576	0.3326	-0.7646	-0.0138	-0.4726	-0.5717	0.1947	0.0299	0.4529	-0.1059	0.0024	0.2899	0.0095	0.2453	20.8191	16.8463	12.5756
16	0.8156	0.1509	-0.0175	1.0497	-0.0635	1.3193	-0.084	0.256	-0.116	-0.7547	0.0709	0.122	0.0596	-0.012	0.0114	0.7735	-0.0699	-0.0907	0.4014	-0.0029	0.3102	9.3514	0.9578	-6.1398
17	0.9318	0.4467	0.1314	2.0702	0.2638	0.7438	-0.0494	0.226	-0.105	-0.5191	0.0367	0.1994	0.2041	-0.0584	-0.0011	0.5494	-0.0404	-0.0998	0.3244	-0.0275	0.2812	7.27	-9.1134	9.019

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 51 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 78 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 79 through 157 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 158 through 209 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 210 through 312 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 313 through 398 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 10 through 209 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 210 through 398 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 10 through 100 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 101 through 157 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 158 through 209 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 210 through 281 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 282 through 399 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 10 through 51 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 52 through 78 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 79 through 157 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 158 through 398 )

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