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

ID or keywords:

Entry

Database: PDB / ID: 8sad

Title

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, PLP/Malonate complex (C2 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 / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate 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, PLP/Malonate complex (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	8sad.cif.gz	334.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8sad.ent.gz	275 KB	Display	PDB format
PDBx/mmJSON format	8sad.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8sad_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8sad_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8sad_validation.xml.gz	36 KB	Display
Data in CIF	8sad_validation.cif.gz	54.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sa/8sad ftp://data.pdbj.org/pub/pdb/validation_reports/sa/8sad	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

hetero molecules

90 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
180 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.589, 130.211, 82.534
Angle α, β, γ (deg.)	90.00, 104.31, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-676- HOH
2	1	A-835- HOH

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Protein , 1 types, 2 molecules AB

#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. PLP and malonate are bound to the sample site with refined occupancy. 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

#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. PLP and malonate are bound to the sample site with refined occupancy.
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

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Non-polymers , 7 types, 682 molecules

#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#7: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.59 Å³/Da / Density % sol: 52.42 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Berkeley G2: 45% MPD, 0.2 M Sodium Malonate, pH 7.0, 0.1 M Bis-Tris, pH 6.5. KlaeA.00906.a.B1.PW39169 at 41.1 mg/mL. Plate: 13119, well G2 drop 3, Puck: PSL-0907, 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: 1.4→79.97 Å / Num. obs: 175389 / % possible obs: 100 % / Redundancy: 6.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.07 / R_pim(I) all: 0.029 / R_rim(I) all: 0.076 / Χ²: 1.02 / Net I/σ(I): 13.5 / Num. measured all: 1209616
Reflection shell	Resolution: 1.4→1.44 Å / % possible obs: 100 % / Redundancy: 6.8 % / R_merge(I) obs: 1.309 / Num. measured all: 87753 / Num. unique obs: 12918 / CC_1/2: 0.599 / R_pim(I) all: 0.54 / R_rim(I) all: 1.419 / 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→42.03 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1612	8645	4.93 %
R_work	0.146	-	-
obs	0.1467	175348	99.96 %

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→42.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6032	0	111	664	6807

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6552
X-RAY DIFFRACTION	f_angle_d	0.854	8944
X-RAY DIFFRACTION	f_dihedral_angle_d	12.888	2337
X-RAY DIFFRACTION	f_chiral_restr	0.068	994
X-RAY DIFFRACTION	f_plane_restr	0.009	1174

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	0.304	308	0.2868	5517	X-RAY DIFFRACTION	100
1.42-1.43	0.2619	291	0.2695	5489	X-RAY DIFFRACTION	100
1.43-1.45	0.2932	301	0.2694	5597	X-RAY DIFFRACTION	100
1.45-1.47	0.2664	277	0.2549	5514	X-RAY DIFFRACTION	100
1.47-1.49	0.2345	287	0.2396	5524	X-RAY DIFFRACTION	100
1.49-1.51	0.2561	285	0.2356	5579	X-RAY DIFFRACTION	100
1.51-1.53	0.2423	286	0.2179	5550	X-RAY DIFFRACTION	100
1.53-1.55	0.2537	288	0.202	5494	X-RAY DIFFRACTION	100
1.55-1.58	0.2186	284	0.2028	5611	X-RAY DIFFRACTION	100
1.58-1.6	0.1983	290	0.196	5555	X-RAY DIFFRACTION	100
1.6-1.63	0.2083	291	0.1858	5513	X-RAY DIFFRACTION	100
1.63-1.66	0.2044	268	0.1772	5533	X-RAY DIFFRACTION	100
1.66-1.69	0.1912	284	0.1667	5563	X-RAY DIFFRACTION	100
1.69-1.73	0.2039	289	0.1694	5548	X-RAY DIFFRACTION	100
1.73-1.76	0.1809	301	0.1616	5579	X-RAY DIFFRACTION	100
1.76-1.8	0.1938	279	0.1603	5522	X-RAY DIFFRACTION	100
1.8-1.85	0.1695	282	0.1537	5572	X-RAY DIFFRACTION	100
1.85-1.9	0.1657	321	0.1469	5552	X-RAY DIFFRACTION	100
1.9-1.96	0.163	299	0.1451	5544	X-RAY DIFFRACTION	100
1.96-2.02	0.1475	272	0.1472	5564	X-RAY DIFFRACTION	100
2.02-2.09	0.1614	272	0.1409	5558	X-RAY DIFFRACTION	100
2.09-2.17	0.1686	306	0.1398	5581	X-RAY DIFFRACTION	100
2.17-2.27	0.156	293	0.1323	5501	X-RAY DIFFRACTION	100
2.27-2.39	0.1361	266	0.1308	5596	X-RAY DIFFRACTION	100
2.39-2.54	0.1407	287	0.1295	5580	X-RAY DIFFRACTION	100
2.54-2.74	0.1316	263	0.1276	5597	X-RAY DIFFRACTION	100
2.74-3.02	0.1553	296	0.1355	5585	X-RAY DIFFRACTION	100
3.02-3.45	0.1499	312	0.1226	5550	X-RAY DIFFRACTION	100
3.45-4.35	0.1134	294	0.1107	5612	X-RAY DIFFRACTION	100
4.35-42.03	0.1444	273	0.1347	5623	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	0.6788	0.1076	0.1018	1.0244	-0.5494	1.5615	0.0671	0.0194	-0.0575	-0.0262	-0.0015	0.0926	0.0433	-0.1824	-0.0702	0.1326	-0.0021	0.0498	0.1582	-0.0044	0.121	27.2171	-11.9012	-5.6242
2	1.637	-0.2597	-0.9657	1.8237	-0.4056	5.4689	0.0793	0.0272	0.0638	-0.0471	-0.0041	0.0567	-0.0951	-0.1425	-0.0681	0.1381	-0.0047	0.0574	0.1243	-0.0051	0.1216	29.4799	-5.1473	-3.5989
3	0.724	0.079	0.1394	0.8276	-0.213	0.6938	-0.0382	-0.1288	0.1508	0.0576	-0.0014	-0.0285	-0.1194	0.0113	0.0352	0.1661	0.0062	0.0612	0.1527	-0.0341	0.1469	38.2308	13.6903	11.9889
4	0.4708	-0.106	0.0487	0.5193	0.0213	0.588	0.004	-0.1379	0.0519	0.0475	-0.0094	0.0528	-0.0676	-0.1108	0.009	0.1686	0.0087	0.0749	0.1983	-0.0166	0.1262	31.8973	3.8953	15.9633
5	1.8768	-0.6701	-1.953	1.8611	1.2522	2.5334	0.1208	0.1861	0.0688	-0.0414	-0.1431	0.0534	-0.1747	-0.1863	0.0032	0.1505	0.0076	0.0522	0.1451	-0.0058	0.1111	33.3203	5.1034	-1.7309
6	0.1427	-0.0318	-0.1689	0.0424	0.0044	0.2114	0.0452	-0.2729	-0.0586	0.0721	0.0196	0.0334	0.0527	-0.0683	0.1386	0.1828	-0.015	0.0882	0.3272	-0.0019	0.0867	35.231	-5.988	27.1909
7	0.8252	-0.1763	0.2394	0.6883	0.0083	0.6844	-0.0326	-0.2031	0.0286	0.0857	0.0195	-0.0927	-0.0163	0.0117	0.0113	0.1914	-0.0161	0.0543	0.2548	-0.0078	0.1184	50.2631	-3.9295	30.0472
8	1.7999	-0.6097	-0.5093	1.3433	0.7749	1.3939	0.059	-0.0906	-0.1027	0.0567	0.0322	-0.0858	0.0811	0.0931	-0.0995	0.1442	-0.0041	0.0139	0.088	0.0194	0.1307	57.705	-25.7354	10.6443
9	0.7503	0.9861	-0.262	2.1687	-0.1788	0.4656	0.1388	-0.0612	-0.2923	-0.0231	0.0361	-0.0266	0.2293	0.0205	-0.1225	0.2188	0.0057	-0.0417	0.1154	0.027	0.2312	50.9224	-36.5009	9.4751
10	0.1279	0.0242	0.0785	0.1935	0.1091	0.1016	0.1679	-0.1563	-0.4201	0.0937	0.0169	0.0342	0.3048	-0.0858	0.2003	0.4783	-0.1968	-0.1885	0.0899	0.2715	0.5372	35.1808	-51.3564	15.7951
11	0.3184	-0.466	-0.0401	2.1259	-1.1705	1.066	0.1487	-0.2292	-0.2586	0.1596	-0.0322	-0.0541	0.0988	-0.1002	-0.1383	0.2325	-0.0671	-0.0437	0.1668	0.0797	0.249	39.6141	-35.7231	14.6306
12	0.781	-0.5951	-0.4254	2.6867	-1.787	2.2302	0.1427	-0.098	-0.3401	0.073	-0.1095	-0.2764	0.2804	0.1484	0.0585	0.2672	-0.0133	-0.1024	0.1296	0.0299	0.3458	51.0963	-43.0302	7.781
13	1.8935	0.9889	-0.8338	0.8088	-0.23	0.5473	0.2741	-0.2065	0.0655	0.1158	-0.0103	0.1385	0.0568	-0.282	-0.0077	0.1927	-0.0741	0.0417	0.2978	0.1035	0.1642	30.5956	-25.6456	18.8753
14	0.2315	0.0172	0.065	0.0031	0.0023	0.02	0.0331	-0.0944	-0.0997	0.0495	0.0349	0.0701	0.0763	-0.1339	-0.0172	0.3244	-0.2202	-0.0217	0.4367	0.2779	0.3124	21.8532	-38.5534	26.0764
15	0.0131	0.0209	-0.0606	1.7488	-1.0262	0.7982	0.2082	-0.3378	-0.361	-0.0267	-0.0183	0.2481	0.2383	-0.2574	-0.1761	0.2606	-0.1159	-0.0234	0.2911	0.1063	0.3368	10.2441	-35.439	9.4923
16	0.5829	-0.0595	0.0164	0.0938	-0.2216	0.5661	0.195	-0.2726	-0.3311	0.0272	-0.013	0.1552	0.1907	-0.1983	-0.0646	0.2631	-0.1316	-0.0164	0.2923	0.113	0.3073	17.3371	-33.4186	11.995

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 47 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 48 through 75 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 76 through 154 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 155 through 226 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 227 through 245 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 246 through 309 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 310 through 395 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 47 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 48 through 97 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 98 through 195 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 196 through 226 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 227 through 245 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 246 through 279 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 280 through 309 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 310 through 330 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 331 through 395 )

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