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

ID or keywords:

Entry

Database: PDB / ID: 8saa

Title

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, PLP and phosphate bound (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 /

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: 1.45 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 and phosphate bound (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	8saa.cif.gz	324.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8saa.ent.gz	265.9 KB	Display	PDB format
PDBx/mmJSON format	8saa.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/8saa ftp://data.pdbj.org/pub/pdb/validation_reports/sa/8saa	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

88.9 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
178 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.092, 131.708, 82.624
Angle α, β, γ (deg.)	90.00, 104.41, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-666- HOH
2	1	B-630- 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-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 790 / 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: 52.72 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpueus C9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaNO3, 30 mM Na2HPO4 and 30 mM (NH4)2SO4, 2mM PLP and 2mM Arginine added to the protein prior to ...Details: Morpueus C9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaNO3, 30 mM Na2HPO4 and 30 mM (NH4)2SO4, 2mM PLP and 2mM Arginine added to the protein prior to crystallization, KlaeA.00906.a.B1.PW39169 at 41.1 mg/mL. Plate: 13220, well C9 drop 3, Puck: PSL-0505, Cryo: Direct

Crystal

Density Matthews: 2.6 Å³/Da / Density % sol: 52.72 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpueus C9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaNO3, 30 mM Na2HPO4 and 30 mM (NH4)2SO4, 2mM PLP and 2mM Arginine added to the protein prior to ...

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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: 1.45→80.03 Å / Num. obs: 156782 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.072 / R_pim(I) all: 0.029 / R_rim(I) all: 0.078 / Χ²: 1.01 / Net I/σ(I): 12.3 / Num. measured all: 1088962
Reflection shell	Resolution: 1.45→1.49 Å / % possible obs: 97.4 % / Redundancy: 6.8 % / R_merge(I) obs: 1.308 / Num. measured all: 77576 / Num. unique obs: 11427 / CC_1/2: 0.724 / R_pim(I) all: 0.539 / R_rim(I) all: 1.417 / Χ²: 1.04 / 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: 1.45→33.48 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1601	7786	4.97 %
R_work	0.1433	-	-
obs	0.1442	156681	98.56 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.45→33.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6002	0	41	790	6833

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6303
X-RAY DIFFRACTION	f_angle_d	0.901	8584
X-RAY DIFFRACTION	f_dihedral_angle_d	12.806	2248
X-RAY DIFFRACTION	f_chiral_restr	0.073	964
X-RAY DIFFRACTION	f_plane_restr	0.01	1119

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 (%)
1.45-1.47	0.2741	261	0.2669	4921	X-RAY DIFFRACTION	97
1.47-1.48	0.2657	249	0.2566	4835	X-RAY DIFFRACTION	97
1.48-1.5	0.2586	273	0.2483	4888	X-RAY DIFFRACTION	97
1.5-1.52	0.2597	240	0.2321	4907	X-RAY DIFFRACTION	98
1.52-1.54	0.2245	251	0.2161	4914	X-RAY DIFFRACTION	97
1.54-1.56	0.2379	256	0.2087	4872	X-RAY DIFFRACTION	98
1.56-1.58	0.2289	247	0.2044	4955	X-RAY DIFFRACTION	98
1.58-1.61	0.2182	255	0.1936	4920	X-RAY DIFFRACTION	98
1.61-1.63	0.1926	271	0.1808	4899	X-RAY DIFFRACTION	98
1.63-1.66	0.2027	232	0.1711	4934	X-RAY DIFFRACTION	98
1.66-1.69	0.2002	265	0.164	4927	X-RAY DIFFRACTION	98
1.69-1.72	0.1809	252	0.1679	4978	X-RAY DIFFRACTION	98
1.72-1.75	0.2072	235	0.1645	4926	X-RAY DIFFRACTION	98
1.75-1.79	0.1909	232	0.1545	4989	X-RAY DIFFRACTION	98
1.79-1.83	0.181	249	0.1487	4960	X-RAY DIFFRACTION	99
1.83-1.87	0.1649	256	0.1445	4967	X-RAY DIFFRACTION	99
1.87-1.92	0.1721	269	0.1385	4955	X-RAY DIFFRACTION	99
1.92-1.97	0.166	261	0.1407	5021	X-RAY DIFFRACTION	99
1.97-2.03	0.1481	286	0.1369	4935	X-RAY DIFFRACTION	99
2.03-2.09	0.1559	248	0.1417	4971	X-RAY DIFFRACTION	99
2.09-2.17	0.1731	275	0.1354	4993	X-RAY DIFFRACTION	99
2.17-2.25	0.1572	229	0.1324	5052	X-RAY DIFFRACTION	99
2.25-2.36	0.1571	283	0.1296	4971	X-RAY DIFFRACTION	99
2.36-2.48	0.1621	257	0.1284	5041	X-RAY DIFFRACTION	100
2.48-2.63	0.1471	272	0.1293	4994	X-RAY DIFFRACTION	100
2.63-2.84	0.1465	255	0.1359	5023	X-RAY DIFFRACTION	99
2.84-3.12	0.151	281	0.142	5017	X-RAY DIFFRACTION	100
3.12-3.57	0.1316	273	0.1361	5048	X-RAY DIFFRACTION	100
3.58-4.5	0.133	286	0.1162	5028	X-RAY DIFFRACTION	100
4.5-33.48	0.1503	287	0.136	5054	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	0.6723	0.3298	-0.2168	1.3848	-1.0411	2.9822	0.0412	0.0136	-0.0129	-0.0523	-0.0028	0.1728	0.0805	-0.2316	-0.0711	0.134	-0.0132	-0.0104	0.1846	-0.0354	0.1893	26.7738	-12.0166	-5.3728
2	0.7582	0.1295	-0.9668	1.4569	-0.087	5.5716	0.0072	-0.0059	0.0421	0.0315	-0.0419	0.1057	-0.0053	-0.2496	0.0051	0.1176	0.0007	-0.0043	0.18	-0.0207	0.1848	28.9261	-5.3723	-3.3403
3	0.5947	-0.2569	-0.1041	1.0376	0.2562	1.3975	0.021	-0.0455	0.0771	0.0722	-0.0211	-0.0266	-0.2163	0.0595	0.0018	0.1664	-0.0145	0.011	0.1558	-0.005	0.1509	38.0209	13.6843	11.925
4	0.8881	-0.3961	-0.0283	1.0415	-0.3557	1.9253	0.0139	-0.031	0.0471	0.1043	-0.0251	0.0871	-0.1565	-0.1732	0.0096	0.1571	-0.0023	0.0307	0.1652	-0.0181	0.1462	29.3206	7.8635	17.745
5	0.3762	-0.1069	-0.2874	0.9931	-0.1692	0.7917	0.0194	0.0434	0.0234	-0.0077	-0.0783	0.006	-0.0055	-0.0443	0.0592	0.1348	-0.0087	-0.0006	0.1709	-0.0185	0.152	35.3315	-0.6535	4.1902
6	0.0923	-0.1297	-0.003	0.4099	0.4617	1.7906	0.0009	-0.0735	-0.0186	0.1415	-0.0137	0.0205	0.1257	-0.0598	0.0181	0.1844	-0.0426	0.0288	0.197	-0.0066	0.1468	34.7191	-6.4885	26.8395
7	0.5926	-0.1905	0.0954	1.6273	0.0789	1.5262	-0.0384	-0.052	0.0178	0.194	0.0111	-0.1593	0.0396	0.1795	0.0299	0.196	-0.0226	-0.0115	0.2159	-0.0021	0.1543	50.0406	-3.6972	30.1615
8	3.6148	-0.2676	-2.007	2.943	-0.146	7.633	-0.0632	-0.1708	-0.0417	0.3416	-0.0501	-0.0341	0.2048	0.0231	0.1409	0.1906	0.0108	-0.0157	0.1048	0.0226	0.1647	49.5617	-22.1665	17.1888
9	0.6055	-0.0084	-0.1418	0.6312	0.0941	0.7764	0.0177	-0.085	-0.1685	0.1185	-0.0589	0.0239	0.334	-0.0027	0.0362	0.3542	-0.014	0.0128	0.1452	0.0346	0.1937	43.158	-43.6772	12.4111
10	4.4935	1.3213	-1.2129	1.0424	-0.3069	1.4779	0.1767	-0.3092	0.0442	0.1823	-0.1653	0.1468	0.0792	-0.1274	-0.0319	0.2202	-0.0566	0.0378	0.1526	-0.007	0.1442	30.0156	-25.758	19.321
11	2.8286	-0.4553	0.0681	0.6968	0.3412	0.2089	0.0221	-0.3394	-0.3742	0.3452	-0.021	0.2868	0.4455	-0.3267	-0.0664	0.4464	-0.1728	0.0883	0.3227	0.0191	0.2718	21.6004	-38.5394	26.1571
12	0.7343	0.1994	0.0404	1.4324	-0.1638	0.4591	0.032	-0.0002	-0.1133	-0.0066	-0.0747	0.2379	0.2901	-0.3473	0.0101	0.3143	-0.1546	0.0517	0.3122	-0.0429	0.266	15.2092	-34.2271	11.4505

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 207 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 208 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 3 through 30 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 31 through 245 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 246 through 279 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 280 through 309 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 310 through 395 )

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