PDB-8sac: Crystal Structure of Cystathionine beta lyase from Klebsiella aer...

ID or keywords:

Entry

Database: PDB / ID: 8sac

Title

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (P21212 form)

Components

Cystathionine beta-lyase

Keywords

LYASE / SSGCID /

STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE

Function / homology

Function and homology information

L-cysteine catabolic process to pyruvate /

cystathionine beta-lyase /

: /

transsulfuration /

pyridoxal phosphate binding /

metal ion binding
Similarity search - Function

Biological species

Klebsiella aerogenes KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (P21212 form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.

History

Deposition	Mar 31, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sac.cif.gz	615.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8sac.ent.gz	511.3 KB	Display	PDB format
PDBx/mmJSON format	8sac.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/sa/8sac ftp://data.pdbj.org/pub/pdb/validation_reports/sa/8sac	HTTPS FTP

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Related structure data

Similar structure data	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 beta-lyase

B: Cystathionine beta-lyase

C: Cystathionine beta-lyase

D: Cystathionine beta-lyase

hetero molecules

177 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)	105.848, 190.810, 79.037
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Cystathionine beta-lyase / Mass: 44102.242 Da / Num. of mol.: 4 / Mutation: V244I, L360P Source method: isolated from a genetically manipulated source Details: Covalent linkage between LYS 210 NZ atom and PLP C4A Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: EAE_03480 / Plasmid: KlaeA.00906.a.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FMF8, cystathionine beta-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-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 815 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.63 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Crystal Screen HT B10: 30% PEG 4000, 0.10 M Tris, pH 8.5, 0.20 M Sodium Acetate. KlaeA.00906.a.B1.PW39169 at 41.1 mg/mL. Plate: 13167, well B10 drop 2, Puck: PSL-0509, Cryo: Direct

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2022
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.8→105.85 Å / Num. obs: 148640 / % possible obs: 100 % / Redundancy: 13.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.095 / R_pim(I) all: 0.027 / R_rim(I) all: 0.099 / Χ²: 1 / Net I/σ(I): 15.5 / Num. measured all: 2018010
Reflection shell	Resolution: 1.8→1.85 Å / % possible obs: 100 % / Redundancy: 13.5 % / R_merge(I) obs: 1.946 / Num. measured all: 146043 / Num. unique obs: 10851 / CC_1/2: 0.69 / R_pim(I) all: 0.549 / R_rim(I) all: 2.023 / Χ²: 1.01 / Net I/σ(I) obs: 1.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_4906: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→60.86 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1923	7280	4.9 %
R_work	0.1649	-	-
obs	0.1662	148510	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.8→60.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11967	0	64	815	12846

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	12570
X-RAY DIFFRACTION	f_angle_d	0.6	17113
X-RAY DIFFRACTION	f_dihedral_angle_d	12.343	4492
X-RAY DIFFRACTION	f_chiral_restr	0.043	1924
X-RAY DIFFRACTION	f_plane_restr	0.006	2232

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 (%)
1.8-1.82	0.3218	229	0.2777	4639	X-RAY DIFFRACTION	100
1.82-1.84	0.2916	257	0.2685	4657	X-RAY DIFFRACTION	100
1.84-1.86	0.2938	242	0.2574	4653	X-RAY DIFFRACTION	100
1.86-1.89	0.306	239	0.242	4681	X-RAY DIFFRACTION	100
1.89-1.91	0.2858	214	0.2273	4661	X-RAY DIFFRACTION	100
1.91-1.94	0.2508	239	0.2139	4677	X-RAY DIFFRACTION	100
1.94-1.97	0.2517	251	0.2091	4673	X-RAY DIFFRACTION	100
1.97-2	0.2586	243	0.2021	4635	X-RAY DIFFRACTION	100
2-2.03	0.2449	248	0.1908	4690	X-RAY DIFFRACTION	100
2.03-2.06	0.2291	256	0.1958	4604	X-RAY DIFFRACTION	100
2.06-2.1	0.2284	256	0.1934	4665	X-RAY DIFFRACTION	100
2.1-2.13	0.2225	244	0.1822	4684	X-RAY DIFFRACTION	100
2.13-2.18	0.2107	215	0.1726	4703	X-RAY DIFFRACTION	100
2.18-2.22	0.2218	217	0.167	4675	X-RAY DIFFRACTION	100
2.22-2.27	0.1728	253	0.1562	4678	X-RAY DIFFRACTION	100
2.27-2.32	0.1913	219	0.1572	4754	X-RAY DIFFRACTION	100
2.32-2.38	0.2084	244	0.1613	4637	X-RAY DIFFRACTION	100
2.38-2.44	0.2129	266	0.158	4668	X-RAY DIFFRACTION	100
2.44-2.51	0.2042	246	0.1646	4681	X-RAY DIFFRACTION	100
2.51-2.6	0.2112	264	0.1686	4691	X-RAY DIFFRACTION	100
2.6-2.69	0.2288	227	0.1748	4729	X-RAY DIFFRACTION	100
2.69-2.8	0.2185	234	0.1871	4725	X-RAY DIFFRACTION	100
2.8-2.92	0.2029	263	0.1843	4701	X-RAY DIFFRACTION	100
2.92-3.08	0.2258	236	0.1825	4728	X-RAY DIFFRACTION	100
3.08-3.27	0.2076	238	0.1824	4744	X-RAY DIFFRACTION	100
3.27-3.52	0.1885	234	0.1692	4773	X-RAY DIFFRACTION	100
3.52-3.88	0.1552	262	0.1427	4738	X-RAY DIFFRACTION	100
3.88-4.44	0.1428	231	0.1255	4818	X-RAY DIFFRACTION	100
4.44-5.59	0.1351	247	0.1192	4856	X-RAY DIFFRACTION	100
5.59-60.86	0.1733	266	0.1654	5012	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	0.5698	0.0927	0.431	1.0486	-1.1493	2.0374	0.0142	0.0932	-0.0362	-0.0749	-0.0095	0.0573	-0.0311	-0.0028	0.0321	0.25	0.0462	0.0328	0.2654	-0.0148	0.2421	34.9095	25.3919	-11.7345
2	1.5551	-0.205	0.3033	1.4997	-0.0528	1.2898	0.1405	0.2106	-0.3179	-0.3972	-0.0614	0.1707	0.382	-0.1222	-0.077	0.4615	0.0144	-0.0729	0.2919	-0.0547	0.3109	22.9782	-1.0711	-20.681
3	0.838	-0.3617	0.14	1.989	-0.2821	1.4331	0.1107	0.1648	-0.1256	-0.3597	-0.0683	-0.0674	0.1778	0.0107	-0.042	0.3525	0.037	-0.0233	0.2975	-0.035	0.3094	32.5738	-0.208	-12.6233
4	3.5253	-1.8462	0.3928	2.7885	-0.3919	1.2091	0.1592	0.2397	0.0197	-0.2726	-0.1194	-0.1381	-0.0013	0.11	-0.0165	0.3298	0.0283	-0.0014	0.3031	-0.0205	0.26	28.0651	14.3135	-19.9063
5	0.5451	-0.3637	0.1357	2.0915	-0.6436	0.8995	0.065	0.0014	-0.1634	-0.0932	-0.0559	0.0321	0.1245	-0.0634	-0.0148	0.2455	0.0167	-0.0185	0.2319	-0.0098	0.298	34.2647	-3.7068	2.2151
6	0.98	0.2773	0.1802	1.5627	0.3851	2.3119	-0.0066	-0.0441	-0.0988	-0.1005	-0.0302	0.4432	0.2331	-0.4336	0.0387	0.278	-0.0304	-0.0381	0.3235	0.0138	0.4648	20.0012	-9.3513	6.0266
7	1.589	-0.1616	0.1561	1.0891	-0.221	0.5084	0.0264	-0.1455	0.0687	0.0353	0.0215	0.0078	-0.0492	-0.1586	-0.0329	0.3062	0.0102	0.0352	0.364	0.0352	0.286	15.9202	19.6816	20.0087
8	0.9472	0.1654	0.4146	0.581	0.2353	1.2658	-0.0286	-0.1231	0.1	0.0691	-0.0022	0.0424	-0.2062	-0.0416	0.0068	0.3346	0.0137	0.0349	0.28	-0.0056	0.2695	37.5578	34.0113	31.0577
9	0.9425	-0.2765	-0.2782	1.2284	0.3522	1.3784	-0.0074	-0.2128	-0.0106	0.0957	0.0697	-0.0627	-0.0041	0.1104	-0.037	0.2659	0.0146	0.0129	0.3007	0.0122	0.2378	42.8881	22.8922	36.3994
10	1.0423	-0.3316	0.044	0.973	0.2406	1.5483	0.0505	-0.0828	-0.0584	0.0097	-0.0111	0.0809	-0.0255	-0.1955	-0.0236	0.2557	0.0087	0.0251	0.2524	0.0097	0.233	29.6704	24.6888	25.6804
11	1.2081	0.0722	-0.1834	0.2093	0.0291	0.5264	0.0114	-0.1025	-0.1314	0.0105	-0.0163	-0.0491	0.0435	0.0299	-0.0207	0.2897	0.0106	0.0072	0.2207	0.0154	0.2998	47.3462	13.3189	18.7302
12	0.7914	0.2542	-0.1175	1.3629	0.3722	1.0367	0.023	-0.008	0.0094	-0.0707	-0.0029	-0.084	-0.1123	0.0746	-0.0066	0.266	0.0066	0.0153	0.2292	0.0161	0.2828	56.4211	24.7622	12.8886
13	2.3628	-0.9902	0.0509	1.1308	0.2598	0.5117	-0.0134	0.0447	0.1771	0.0813	-0.0368	-0.2033	-0.1084	0.0672	0.0517	0.3752	0.0075	0.0429	0.2922	0.0155	0.3071	34.9682	40.0801	2.4333
14	1.3354	-0.1674	0.2197	0.6544	-0.1879	1.6057	-0.0579	-0.1432	0.254	0.1155	0.0342	0.041	-0.3657	-0.1654	0.0137	0.4147	0.0907	0.0283	0.2913	-0.0358	0.3156	20.6466	53.0989	23.668
15	0.6851	-0.1115	0.292	0.832	0.1099	1.2592	0.0531	-0.0818	0.0273	0.0456	-0.0062	0.0269	-0.1067	-0.0115	-0.052	0.3267	0.0617	0.0425	0.2609	0.0017	0.2595	27.0004	42.5938	14.4394
16	0.9958	0.2613	-0.2312	0.3973	0.1303	0.8307	0.0458	0.0339	0.2609	0.0096	-0.0247	0.1574	-0.2454	-0.3461	-0.0136	0.3311	0.1376	0.04	0.3713	0.0219	0.3391	4.8149	49.3615	9.1072
17	1.3008	0.0697	0.5686	1.0362	0.0036	0.6382	0.0104	-0.1832	-0.0059	0.0927	-0.0467	0.2266	-0.0097	-0.3581	0.0565	0.3619	0.1106	0.0884	0.5092	0.0149	0.3622	-2.6669	40.8803	19.9599
18	1.7114	-0.7782	-0.3205	3.0772	-0.3322	1.0993	0.0631	0.0511	-0.262	-0.0099	-0.0519	0.1422	0.1887	-0.1706	-0.0324	0.2851	-0.0177	0.0037	0.3921	0.0106	0.3551	6.956	15.5023	5.4469
19	2.1486	-1.3566	1.016	4.691	-0.7298	3.5464	-0.0789	0.1302	-0.7398	-0.0184	0.0583	0.1768	0.6567	0.029	0.026	0.3995	-0.0332	0.0566	0.499	0.019	0.5063	6.755	14.2711	-2.2348
20	0.7342	-0.2318	0.1724	1.0083	-0.1011	1.549	0.0678	0.1252	-0.0549	-0.1784	0.0143	0.2434	0.1453	-0.2982	-0.0874	0.2866	0.0092	-0.0554	0.3953	0.007	0.3274	5.6176	21.0418	-22.6492
21	0.793	-0.1087	-0.0195	0.8555	-0.396	1.3504	0.0833	0.188	0.102	-0.0764	0.0068	0.0559	-0.2253	-0.1689	-0.0805	0.2994	0.1061	0.0167	0.3479	0.0145	0.2628	13.6513	42.8513	-21.3069

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 75 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 76 through 154 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 155 through 220 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 221 through 245 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 246 through 309 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 310 through 395 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 5 through 75 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 76 through 132 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 133 through 195 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 196 through 245 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 246 through 309 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 310 through 395 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 4 through 75 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 76 through 207 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 208 through 245 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 246 through 309 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 310 through 395 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 5 through 47 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 48 through 75 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 76 through 245 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 246 through 395 )

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