PDB-8duy: Crystal structure of Cystathionine beta-lyase from Klebsiella pne...

ID or keywords:

Entry

Database: PDB / ID: 8duy

Title

Crystal structure of Cystathionine beta-lyase from Klebsiella pneumoniae

Components

Cystathionine beta-lyase

Keywords

LYASE / SSGCID / Klebsiella pneumoniae / Cystathionine beta-lyase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

cystathionine beta-lyase / : / transsulfuration / pyridoxal phosphate binding
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To be Published
Title: Crystal Structure of Cystathionine beta-lyase from Klebsiella pneumoniae
Authors: Dranow, D.M. / Abendroth, J.A. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jul 27, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 10, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8duy.cif.gz	643.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8duy.ent.gz	524.1 KB	Display	PDB format
PDBx/mmJSON format	8duy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8duy_validation.pdf.gz	465.3 KB	Display	wwPDB validaton report
Full document	8duy_full_validation.pdf.gz	475.6 KB	Display
Data in XML	8duy_validation.xml.gz	73.5 KB	Display
Data in CIF	8duy_validation.cif.gz	108.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/du/8duy ftp://data.pdbj.org/pub/pdb/validation_reports/du/8duy	HTTPS FTP

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Related structure data

Related structure data	2fq6S S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: KlpnC.00906.a

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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

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

1

A: Cystathionine beta-lyase

D: Cystathionine beta-lyase

hetero molecules

defined by author&software
Evidence: gel filtration
89.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cystathionine beta-lyase

C: Cystathionine beta-lyase

hetero molecules

defined by author&software
89.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.610, 131.140, 85.440
Angle α, β, γ (deg.)	90.000, 99.930, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cystathionine beta-lyase / Cystathionine beta-lyase MetC Mass: 44499.395 Da / Num. of mol.: 4 / Fragment: KlpnC.00906.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPHS_45550 / Plasmid: KlpnC.00906.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0ZBA0, cystathionine beta-lyase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1682 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52.22 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1:1 27 mg/mL KlpnC.00906.a.B1.PW38994 to JCSG_TOP96(a5) (40% v/v MPD, 100 mM HEPES free acid/ NaOH, pH 6.5), harvested and frozen directly, puck: yis2-8, barcode: 321997a5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 29, 2021 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.9→45.91 Å / Num. obs: 140666 / % possible obs: 99.9 % / Redundancy: 7.502 % / B_iso Wilson estimate: 15.37 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.126 / R_rim(I) all: 0.135 / Χ²: 0.932 / Net I/σ(I): 14.94 / Num. measured all: 1055272 / Scaling rejects: 31

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.9-1.95	7.596	0.591	4.81	10364	0.9	0.634	99.9
1.95-2	7.595	0.48	5.83	10127	0.929	0.515	100
2-2.06	7.605	0.404	6.73	9852	0.944	0.433	100
2.06-2.12	7.609	0.346	7.76	9584	0.962	0.371	99.9
2.12-2.19	7.616	0.292	8.93	9221	0.968	0.314	100
2.19-2.27	7.623	0.248	10.15	8970	0.977	0.267	100
2.27-2.36	7.616	0.216	11.27	8670	0.983	0.231	99.9
2.36-2.45	7.623	0.191	12.47	8325	0.985	0.205	100
2.45-2.56	7.621	0.175	13.25	7978	0.989	0.188	100
2.56-2.69	7.595	0.143	15.45	7631	0.991	0.153	99.9
2.69-2.83	7.573	0.122	17.43	7291	0.992	0.131	100
2.83-3	7.543	0.103	19.69	6856	0.994	0.111	100
3-3.21	7.453	0.087	22.3	6490	0.995	0.094	99.9
3.21-3.47	7.362	0.073	25.31	6016	0.997	0.079	99.9
3.47-3.8	7.258	0.064	27.65	5530	0.997	0.069	99.9
3.8-4.25	7.189	0.059	29.81	5044	0.996	0.064	100
4.25-4.91	7.076	0.057	31.08	4441	0.997	0.062	99.9
4.91-6.01	7.123	0.06	30.02	3766	0.997	0.065	100
6.01-8.5	7.049	0.059	30.52	2917	0.997	0.064	99.9
8.5-45.91	6.372	0.057	32.16	1593	0.997	0.062	97.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487	refinement
XDS		data reduction
PDB_EXTRACT	3.27	data extraction
XSCALE		data scaling
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2FQ6

2fq6

Resolution: 1.9→45.91 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1954	2090	1.49 %
R_work	0.1632	138538	-
obs	0.1637	140628	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 61.58 Å² / B_iso mean: 17.7046 Å² / B_iso min: 5.83 Å²

Refinement step

Cycle: final / Resolution: 1.9→45.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12066	0	32	1701	13799
B_iso mean	-	-	35.36	25.97	-
Num. residues	-	-	-	-	1566

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.9-1.94	0.2378	152	0.1815	9172	9324
1.94-1.99	0.2056	133	0.1711	9197	9330
1.99-2.05	0.2381	132	0.1626	9246	9378
2.05-2.11	0.1894	136	0.1549	9229	9365
2.11-2.17	0.1798	140	0.1526	9224	9364
2.17-2.25	0.1899	125	0.1518	9206	9331
2.25-2.34	0.1908	112	0.155	9249	9361
2.34-2.45	0.2202	147	0.1576	9215	9362
2.45-2.58	0.206	163	0.1667	9244	9407
2.58-2.74	0.2009	137	0.1638	9216	9353
2.74-2.95	0.2193	141	0.1689	9227	9368
2.95-3.25	0.2033	135	0.1684	9228	9363
3.25-3.72	0.1908	132	0.1612	9287	9419
3.72-4.68	0.1633	157	0.15	9264	9421
4.68-45.91	0.184	148	0.1821	9334	9482

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	2.2073	0.1428	0.0175	0.7571	-0.1946	0.3824	0.0299	0.2956	-0.0245	-0.1251	-0.0561	-0.0159	0.0631	0.0281	0.0275	0.1294	0.0357	0.0028	0.1462	0.0106	0.0618	-6.4368	10.0568	4.3807
2	1.2599	-0.5988	0.2754	1.3405	-0.6607	0.5018	0.0428	0.0526	-0.1345	0.0239	-0.0327	0.0588	0.02	0.0105	-0.0085	0.0995	0.007	-0.0011	0.0816	-0.0167	0.0686	3.5399	-10.4877	21.2148
3	4.0413	1.9172	-0.2657	6.4916	1.0138	2.6046	0.0686	0.0906	-0.3009	0.0478	-0.0345	-0.2119	0.4778	0.2088	-0.006	0.1427	0.0405	-0.0012	0.1298	0.01	0.0511	14.1149	-17.531	17.0713
4	1.0809	-0.2155	0.0174	0.6581	-0.1827	0.3693	0.0993	0.2326	-0.0376	-0.0961	-0.1104	-0.0632	0.0917	0.0579	0.0138	0.1054	0.0352	0.0075	0.1208	0.0027	0.0725	7.9963	-2.9227	13.7769
5	1.5148	-0.3064	0.5501	0.4688	-0.1635	0.6324	0.0441	0.2201	0.2251	-0.0521	-0.0588	-0.1575	0.0012	0.1295	0.0339	0.1003	0.0041	0.0133	0.093	0.043	0.1383	17.1026	13.4705	18.307
6	1.0188	-0.2531	0.1692	0.9217	0.398	0.6259	-0.0051	-0.0051	0.0665	0.1157	0.0199	-0.0914	0.0426	0.0195	-0.0241	0.0868	-0.0079	-0.015	0.1186	0.0324	0.1265	23.0747	4.4127	31.3631
7	1.1023	0.9649	-0.9368	1.0456	-0.5117	1.5164	-0.0017	0.3433	0.0691	-0.1481	-0.0271	0.0158	0.0259	-0.0608	0.0179	0.1239	0.0357	-0.0122	0.1422	0.039	0.1038	-13.5551	26.1346	4.0762
8	0.6948	-0.3617	-0.1473	0.8649	0.4449	0.4087	-0.0029	0.0336	0.1018	0.0069	-0.0249	-0.0546	-0.0813	0.0336	0.0205	0.1593	0.0032	-0.0107	0.0991	0.0517	0.1231	-14.4273	45.0563	16.7846
9	1.9357	1.0065	-0.7294	3.3632	-1.1881	2.2963	0.1446	-0.0135	0.369	0.1229	-0.186	0.0326	-0.3515	-0.0683	0.0386	0.2336	0.0566	-0.0274	0.1413	0.0132	0.1901	-26.5966	58.12	22.7144
10	0.5324	-0.0268	-0.2562	0.4758	0.0376	0.6494	-0.0035	0.0748	0.1663	0.0044	-0.0466	-0.0132	-0.1413	-0.0727	0.0574	0.1485	0.0289	-0.0216	0.0967	0.0203	0.1368	-22.4094	43.3478	18.643
11	0.7667	0.0019	-0.6595	0.5267	0.0015	1.5695	-0.0577	-0.0415	0.0864	0.0797	0.0273	0.1218	-0.0043	-0.1652	0.0279	0.1028	0.0166	-0.0128	0.1049	-0.0236	0.1116	-32.2732	33.4808	30.892
12	0.8204	0.0783	-0.2191	1.3424	0.2184	1.197	-0.0041	-0.1217	0.0522	0.1707	-0.0632	0.0173	-0.1193	-0.0175	0.0604	0.1592	0.0187	-0.0046	0.1327	-0.0344	0.1009	-24.6093	36.9507	44.2842
13	2.9027	-1.1531	-1.1306	0.8625	0.4454	1.3169	-0.0241	-0.1093	0.1207	0.0754	-0.015	-0.0844	-0.0451	0.0513	0.0152	0.1435	-0.0175	-0.0247	0.0924	0.0114	0.1164	0.8387	27.5538	35.8604
14	2.184	0.4223	-0.954	0.9818	-0.5931	1.3364	-0.0361	-0.2193	0.24	0.0364	-0.001	-0.0207	-0.0829	0.126	0.0278	0.1697	-0.0135	-0.0218	0.1225	-0.0075	0.1638	1.4561	34.5728	32.9537
15	0.5834	0.209	-0.1572	1.0985	-0.6944	1.194	-0.0096	0.0486	0.1315	0.0676	-0.0373	-0.1005	-0.0937	0.1145	0.0463	0.1535	-0.0152	-0.0238	0.1092	0.0594	0.1877	2.9787	50.8723	14.9066
16	0.8772	0.2433	-0.2053	0.9338	0.1004	0.6752	0.0762	0.0215	0.1804	0.0426	-0.2005	-0.212	-0.2094	0.0804	0.0775	0.1736	-0.0672	-0.0384	0.1914	0.0965	0.2771	16.0971	50.8758	15.5083
17	0.5257	-0.1371	-0.2536	0.9737	-0.0927	0.7809	-0.0028	-0.0563	0.0935	0.0307	-0.0511	-0.1434	-0.1257	0.1026	0.0509	0.1325	-0.0225	-0.0253	0.1133	0.0504	0.1736	5.3915	40.3454	22.328
18	0.3537	0.1291	-0.3154	0.4831	-0.1015	0.8759	0.0228	0.1769	0.1189	-0.0412	-0.0956	-0.2397	-0.0607	0.179	0.0542	0.0989	0.0057	0.0187	0.22	0.1317	0.2673	19.8369	32.0796	8.5906
19	0.3609	0.1908	-0.0482	0.8545	0.1421	0.5314	0.0434	0.2175	0.1225	-0.265	-0.1686	-0.0327	-0.0575	0.1622	0.0694	0.1962	0.0301	0.0483	0.2783	0.1484	0.2124	12.1462	34.2413	-5.1326
20	3.4044	-0.5295	0.0534	0.9556	0.1045	0.4388	-0.0602	-0.2517	0.0666	0.0762	0.0182	-0.0667	-0.0321	0.0137	0.0368	0.1413	-0.008	-0.0022	0.097	-0.0022	0.0528	-6.2657	11.7099	37.5377
21	1.209	0.1271	0.0996	1.1909	0.136	0.6834	0.0002	0.1215	-0.2989	-0.0313	0.0472	0.0322	0.0623	-0.033	-0.0391	0.0938	0.0083	-0.007	0.0762	-0.0268	0.1177	-15.9918	-10.3778	22.7016
22	1.3985	0.0353	0.0256	0.6058	-0.1095	0.5324	0.0319	-0.1143	-0.1737	0.0786	-0.0283	0.0567	0.0385	-0.0485	-0.0075	0.0897	-0.0066	-0.0002	0.0829	-0.0079	0.0925	-21.8277	-5.0206	29.1225
23	1.0367	0.1321	0.3285	0.3923	-0.1063	0.4128	0.029	0.1226	-0.0312	-0.0574	0.0056	0.0991	0.0322	-0.0686	-0.0194	0.0865	0.013	-0.0104	0.1167	-0.0344	0.1137	-34.1585	6.0307	14.0125

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 75 )	A	5 - 75
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 76 through 132 )	A	76 - 132
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 133 through 154 )	A	133 - 154
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 155 through 245 )	A	155 - 245
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 246 through 279 )	A	246 - 279
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 280 through 395 )	A	280 - 395
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 4 through 47 )	B	4 - 47
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 48 through 132 )	B	48 - 132
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 133 through 154 )	B	133 - 154
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 155 through 245 )	B	155 - 245
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 246 through 309 )	B	246 - 309
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 310 through 395 )	B	310 - 395
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 5 through 47 )	C	5 - 47
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 48 through 75 )	C	48 - 75
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 76 through 132 )	C	76 - 132
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 133 through 195 )	C	133 - 195
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 196 through 245 )	C	196 - 245
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 246 through 309 )	C	246 - 309
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 310 through 395 )	C	310 - 395
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 4 through 75 )	D	4 - 75
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 76 through 132 )	D	76 - 132
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 133 through 245 )	D	133 - 245
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 246 through 395 )	D	246 - 395

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi