PDB-8sa7: Crystal Structure of Cystathionine beta lyase from Klebsiella aer...

ID or keywords:

Entry

Database: PDB / ID: 8sa7

Title

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (C2 form)

Components

Cystathionine beta-lyase

Keywords

LYASE / SSGCID /

STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE /

LIGASE

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: 1.4 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 (C2 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	8sa7.cif.gz	336.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8sa7.ent.gz	276.2 KB	Display	PDB format
PDBx/mmJSON format	8sa7.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/8sa7 ftp://data.pdbj.org/pub/pdb/validation_reports/sa/8sa7	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
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Cystathionine beta-lyase

B: Cystathionine beta-lyase

hetero molecules

89.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cystathionine beta-lyase

B: Cystathionine beta-lyase

hetero molecules

A: Cystathionine beta-lyase

B: Cystathionine beta-lyase

hetero molecules

defined by author&software
Evidence: gel filtration
179 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.291, 131.297, 82.686
Angle α, β, γ (deg.)	90.00, 104.26, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-674- HOH
2	1	A-871- HOH
3	1	B-651- HOH
4	1	B-840- HOH

#1: Protein	Cystathionine beta-lyase / Mass: 44102.242 Da / Num. of mol.: 2 / 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-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-BR / BROMIDE ION / Bromide Mass: 79.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Br
#4: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.6 Å³/Da / Density % sol: 52.75 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpueus B9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. 2mM PLP and 2mM Lysine added to protein prior to crystallization, ...Details: Morpueus B9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. 2mM PLP and 2mM Lysine added to protein prior to crystallization, KlaeA.00906.a.B1.PW39169 at 41.1 mg/mL. Plate: 13219 well B9 drop 3, Puck: PSL-0408, Cryo: Direct

Crystal

Density Matthews: 2.6 Å³/Da / Density % sol: 52.75 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpueus B9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. 2mM PLP and 2mM Lysine added to protein prior to crystallization, ...

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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: 1.4→71.12 Å / Num. obs: 170459 / % possible obs: 96.6 % / Redundancy: 7.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.065 / R_pim(I) all: 0.026 / R_rim(I) all: 0.07 / Χ²: 1.01 / Net I/σ(I): 12.9 / Num. measured all: 1209660
Reflection shell	Resolution: 1.4→1.44 Å / % possible obs: 94.4 % / Redundancy: 7.2 % / R_merge(I) obs: 1.382 / Num. measured all: 89113 / Num. unique obs: 12326 / CC_1/2: 0.661 / R_pim(I) all: 0.549 / R_rim(I) all: 1.488 / Χ²: 1.05 / Net I/σ(I) obs: 1.5

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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: 1.4→26.44 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1582	8469	4.97 %
R_work	0.1396	-	-
obs	0.1405	170361	96.44 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.4→26.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5988	0	44	775	6807

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6542
X-RAY DIFFRACTION	f_angle_d	1.095	8939
X-RAY DIFFRACTION	f_dihedral_angle_d	13	2365
X-RAY DIFFRACTION	f_chiral_restr	0.083	990
X-RAY DIFFRACTION	f_plane_restr	0.012	1184

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 (%)
1.4-1.42	0.3035	255	0.2784	5301	X-RAY DIFFRACTION	94
1.42-1.43	0.2695	311	0.2678	5255	X-RAY DIFFRACTION	94
1.43-1.45	0.2933	273	0.2536	5229	X-RAY DIFFRACTION	94
1.45-1.47	0.2792	265	0.2413	5292	X-RAY DIFFRACTION	95
1.47-1.49	0.2268	266	0.226	5315	X-RAY DIFFRACTION	95
1.49-1.51	0.2405	286	0.2238	5254	X-RAY DIFFRACTION	95
1.51-1.53	0.2475	251	0.2091	5334	X-RAY DIFFRACTION	95
1.53-1.55	0.2071	284	0.1937	5317	X-RAY DIFFRACTION	95
1.55-1.58	0.2024	284	0.1872	5336	X-RAY DIFFRACTION	95
1.58-1.6	0.2076	279	0.1835	5311	X-RAY DIFFRACTION	95
1.6-1.63	0.1909	253	0.1712	5366	X-RAY DIFFRACTION	96
1.63-1.66	0.1907	304	0.1607	5276	X-RAY DIFFRACTION	96
1.66-1.69	0.1764	309	0.152	5337	X-RAY DIFFRACTION	96
1.69-1.73	0.1732	267	0.152	5375	X-RAY DIFFRACTION	96
1.73-1.76	0.1801	265	0.1481	5410	X-RAY DIFFRACTION	96
1.76-1.8	0.1578	278	0.1399	5374	X-RAY DIFFRACTION	96
1.8-1.85	0.1751	288	0.1414	5418	X-RAY DIFFRACTION	97
1.85-1.9	0.1536	267	0.1372	5449	X-RAY DIFFRACTION	97
1.9-1.96	0.1611	282	0.1373	5371	X-RAY DIFFRACTION	97
1.96-2.02	0.1475	293	0.1315	5481	X-RAY DIFFRACTION	97
2.02-2.09	0.1452	276	0.1342	5421	X-RAY DIFFRACTION	98
2.09-2.17	0.1463	255	0.1276	5485	X-RAY DIFFRACTION	97
2.17-2.27	0.1515	320	0.1221	5418	X-RAY DIFFRACTION	98
2.27-2.39	0.1433	270	0.1219	5530	X-RAY DIFFRACTION	98
2.39-2.54	0.1469	297	0.1247	5498	X-RAY DIFFRACTION	98
2.54-2.74	0.1511	323	0.1243	5469	X-RAY DIFFRACTION	98
2.74-3.01	0.148	285	0.1353	5511	X-RAY DIFFRACTION	98
3.01-3.45	0.1564	282	0.1342	5586	X-RAY DIFFRACTION	99
3.45-4.34	0.1169	289	0.121	5592	X-RAY DIFFRACTION	99
4.34-26.44	0.1573	312	0.1285	5581	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	0.6818	0.1123	0.1613	1.3892	-0.1031	0.7808	0.1067	-0.1059	-0.1361	-0.0364	-0.0599	0.2079	0.2282	-0.3102	-0.0508	0.28	-0.1288	0.0095	0.3	0.0112	0.2419	15.5263	-34.2288	11.3771
2	0.7149	0.3514	-0.2994	1.3899	-1.638	4.4758	0.0478	0.0169	-0.0383	-0.0483	0.041	0.1567	0.0618	-0.2952	-0.1214	0.1301	-0.0078	-0.0049	0.1577	-0.0269	0.1627	26.9018	-11.8589	-5.9248
3	1.5782	-0.119	-1.8792	1.7911	-0.0517	7.9893	0.0353	0.033	0.0529	0.0247	-0.0244	0.1296	-0.0451	-0.3295	-0.0232	0.0958	-0.0041	0.001	0.129	-0.0134	0.1438	28.787	-5.5056	-3.1104
4	0.6403	-0.2465	-0.0276	0.8303	0.1293	0.9002	0.0152	-0.0322	0.1039	0.0569	-0.0164	-0.0155	-0.1569	0.066	0.0029	0.19	-0.0132	0.0206	0.1699	-0.0026	0.1701	40.196	11.8286	9.3878
5	0.3258	-0.2321	0.2222	1.1009	-0.4217	1.1917	-0.0185	-0.0765	0.0489	0.1129	-0.0166	0.0714	-0.1701	-0.1118	0.0286	0.203	0.0189	0.0387	0.195	-0.0275	0.1639	30.8887	12.0445	18.7435
6	0.7359	-0.7318	0.352	1.7254	-0.1592	0.6023	-0.0074	-0.0594	-0.0145	0.0614	0.007	0.0727	-0.0082	-0.0802	0.0027	0.1504	-0.0095	0.0196	0.1602	-0.0043	0.132	34.6541	-3.2662	12.5736
7	1.5465	-0.4497	-1.1793	1.6591	0.4203	1.9049	0.0467	0.0876	0.0474	-0.0329	-0.0707	0.0398	-0.0637	-0.1171	0.0178	0.1512	0.0004	0.0023	0.171	-0.0127	0.1458	32.4695	4.3334	-0.1223
8	0.0645	-0.0989	0.1008	0.3489	0.3228	1.492	0.0071	-0.0898	-0.0112	0.1157	-0.0036	0.0218	0.0817	-0.06	0.0019	0.1864	-0.0358	0.035	0.2101	-0.0046	0.1375	35.0818	-6.1685	27.3474
9	0.5155	-0.2132	0.0451	1.6975	0.0353	0.8544	-0.0031	-0.0617	0.0232	0.1371	-0.001	-0.203	-0.0047	0.1589	0.0108	0.2158	-0.0283	0.0062	0.2335	-0.0088	0.1714	51.9471	-3.5221	28.1476
10	0.6842	-0.2113	0.194	2.1205	-0.112	1.675	-0.0116	-0.1139	0.0187	0.258	-0.007	-0.0693	0.0414	0.0888	0.0235	0.19	-0.0153	0.0087	0.225	-0.0118	0.135	47.7106	-4.0665	31.9768
11	2.3361	-1.3659	-1.3102	1.4666	1.2885	1.9165	-0.0322	-0.089	-0.008	0.0864	0.0243	-0.1033	0.1449	0.1354	0.0222	0.1725	-0.0002	-0.0102	0.1133	0.0267	0.1386	57.0715	-25.8432	10.8091
12	0.9528	0.4254	-0.0354	1.0183	-0.0606	0.7272	0.088	-0.0637	-0.1322	0.0824	-0.0368	-0.064	0.203	0.0701	-0.0479	0.2537	0.0145	-0.0194	0.132	0.0194	0.172	50.7058	-36.4362	9.9093
13	0.6329	0.0099	-0.2422	0.3669	-0.0834	0.7507	0.0486	-0.0921	-0.2784	0.1704	-0.0523	0.0652	0.4317	-0.1077	-0.0187	0.4603	-0.0746	-0.0359	0.1931	0.064	0.295	35.0779	-51.6033	16.0346
14	1.0274	-0.5269	0.3419	1.3218	0.071	0.4898	0.0631	-0.1535	-0.1396	0.1365	0.0058	0.0476	0.1922	-0.0549	-0.0832	0.2576	-0.0418	0.0006	0.1626	0.0261	0.1751	38.3593	-35.0172	14.5429
15	1.3303	-0.006	-1.0064	1.8862	-0.4039	3.8924	0.057	-0.1176	-0.2156	0.0698	-0.0435	-0.0508	0.3905	0.1868	-0.0064	0.2767	-0.003	-0.0357	0.1495	0.0213	0.214	50.0071	-42.6735	9.1242
16	5.6835	1.5823	-2.0309	1.0184	-0.5416	2.2279	0.2038	-0.2972	0.0795	0.1314	-0.1337	0.1393	0.0496	-0.16	-0.0922	0.1969	-0.0471	0.0201	0.1438	0.0103	0.1289	30.3621	-25.5921	19.3124
17	2.454	0.0623	-0.1721	0.7246	0.4008	0.2421	0.0928	-0.3132	-0.3512	0.2694	0.0095	0.172	0.3807	-0.3448	-0.078	0.3908	-0.1681	0.0176	0.3423	0.074	0.2446	21.4042	-38.6966	25.9989

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 310 through 395 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 5 through 47 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 75 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 76 through 132 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 133 through 195 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 196 through 220 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 221 through 245 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 246 through 309 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 310 through 358 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 359 through 395 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 5 through 47 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 48 through 97 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 98 through 195 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 196 through 220 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 221 through 245 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 246 through 279 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 280 through 309 )

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