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- PDB-9axj: Cystathionine gamma lyase from Thermobifida fusca in an amino cro... -

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Open data

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Basic information

Entry

Database: PDB / ID: 9axj

Title

Cystathionine gamma lyase from Thermobifida fusca in an amino crotonate form

Components

Cystathionine gamma-synthase

Keywords

LYASE / PLP / amino crotonate

Function / homology

Function and homology information

carbon-sulfur lyase activity / cystathionine gamma-synthase / cystathionine gamma-synthase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function

Biological species

Thermobifida fusca (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Perkins, L.J. / Zmich, A.P. / Bingman, C.A. / Buller, A.R.

Funding support

United States, 1items

Citation

Journal: Acs Catalysis / Year: 2024
Title: Elucidation of the stereochemical mechanism of cystathionine gamma-lyase reveals how substrate specificity constrains catalysis.
Authors: Zmich, A. / Perkins, L.J. / Bingman, C. / Buller, A.R.

History

Deposition	Mar 6, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	9axj.cif.gz	161.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9axj.ent.gz	122.6 KB	Display	PDB format
PDBx/mmJSON format	9axj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9axj_validation.pdf.gz	791.2 KB	Display	wwPDB validaton report
Full document	9axj_full_validation.pdf.gz	793.7 KB	Display
Data in XML	9axj_validation.xml.gz	22.4 KB	Display
Data in CIF	9axj_validation.cif.gz	33.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ax/9axj ftp://data.pdbj.org/pub/pdb/validation_reports/ax/9axj	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

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Assembly

Deposited unit

A: Cystathionine gamma-synthase

hetero molecules

42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cystathionine gamma-synthase

hetero molecules

A: Cystathionine gamma-synthase

hetero molecules

A: Cystathionine gamma-synthase

hetero molecules

A: Cystathionine gamma-synthase

hetero molecules

defined by author&software
169 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.946, 116.946, 116.946
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	195
Space group name H-M	P23

Components on special symmetry positions

ID	Model	Components
1	1	A-719- HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein	Cystathionine gamma-synthase Mass: 41551.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (bacteria) / Gene: Tfu_0440 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A9P2TCP3, cystathionine gamma-synthase

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Non-polymers , 5 types, 384 molecules

#2: Chemical	ChemComp-4LM / (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid Mass: 330.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₅N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experimental details

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 3.24 Å³/Da / Density % sol: 62.07 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: Well solution comprising 20-30% PEG300, 0.1 M HEPES, 0.2 M MgCl2. 2 uL drops were laid with a 1:1 mixture of well solution and 8 mg/mL protein in 0.1 M HEPES buffer pH 7.0. Crystals were ...
PH range: 7.0-7.5

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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 MX300HE / Detector: CCD / Date: Jul 28, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.5→40 Å / Num. obs: 84295 / % possible obs: 99 % / Redundancy: 21.6 % / CC_1/2: 1 / R_pim(I) all: 0.02 / Net I/σ(I): 21.2
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 15.7 % / Num. unique obs: 4184 / CC_1/2: 0.333 / R_pim(I) all: 0.93 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→39.012 Å / Cor.coef. F_o:F_c: 0.983 / Cor.coef. F_o:F_c free: 0.979 / SU B: 2.171 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.047 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.156	4113	4.88 %
R_work	0.1371	80163	-
all	0.138	-	-
obs	-	84276	98.991 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 22.288 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0 Å²	0 Å²
3-	-	-	0 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→39.012 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2820	0	34	377	3231

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.013	3068
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2870
X-RAY DIFFRACTION	r_angle_refined_deg	1.89	1.638	4206
X-RAY DIFFRACTION	r_angle_other_deg	1.609	1.571	6613
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.637	5	412
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.499	20.364	165
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.067	15	471
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.567	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	396
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	3623
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	669
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	628
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.178	0.2	2642
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	1489
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1334
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	229
X-RAY DIFFRACTION	r_metal_ion_refined	0.087	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.163	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	111
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.18	0.2	38
X-RAY DIFFRACTION	r_mcbond_it	0.895	1.429	1594
X-RAY DIFFRACTION	r_mcbond_other	0.893	1.428	1593
X-RAY DIFFRACTION	r_mcangle_it	1.229	2.142	2018
X-RAY DIFFRACTION	r_mcangle_other	1.229	2.142	2019
X-RAY DIFFRACTION	r_scbond_it	1.794	1.617	1474
X-RAY DIFFRACTION	r_scbond_other	1.794	1.619	1475
X-RAY DIFFRACTION	r_scangle_it	2.615	2.357	2186
X-RAY DIFFRACTION	r_scangle_other	2.614	2.359	2187
X-RAY DIFFRACTION	r_lrange_it	5.071	18.907	3472
X-RAY DIFFRACTION	r_lrange_other	4.891	17.994	3393

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 (%)
1.5-1.539	0.307	307	0.299	5910	X-RAY DIFFRACTION	100
1.539-1.581	0.259	299	0.255	5815	X-RAY DIFFRACTION	100
1.581-1.627	0.238	322	0.223	5571	X-RAY DIFFRACTION	100
1.627-1.677	0.254	290	0.205	5469	X-RAY DIFFRACTION	100
1.677-1.732	0.198	277	0.179	5294	X-RAY DIFFRACTION	100
1.732-1.792	0.176	247	0.159	5147	X-RAY DIFFRACTION	100
1.792-1.86	0.158	266	0.147	4954	X-RAY DIFFRACTION	100
1.86-1.936	0.161	228	0.129	4773	X-RAY DIFFRACTION	100
1.936-2.021	0.176	196	0.125	4624	X-RAY DIFFRACTION	99.9793
2.021-2.12	0.15	217	0.115	4391	X-RAY DIFFRACTION	100
2.12-2.234	0.147	220	0.116	4196	X-RAY DIFFRACTION	100
2.234-2.369	0.133	137	0.117	3196	X-RAY DIFFRACTION	80.5462
2.369-2.532	0.142	189	0.114	3741	X-RAY DIFFRACTION	100
2.532-2.734	0.127	176	0.112	3465	X-RAY DIFFRACTION	100
2.734-2.994	0.148	157	0.124	3212	X-RAY DIFFRACTION	100
2.994-3.345	0.15	202	0.136	2879	X-RAY DIFFRACTION	100
3.345-3.858	0.148	125	0.131	2596	X-RAY DIFFRACTION	100
3.858-4.714	0.119	108	0.112	2166	X-RAY DIFFRACTION	98.1018
4.714-6.62	0.157	87	0.136	1744	X-RAY DIFFRACTION	100
6.62-39	0.13	63	0.145	1020	X-RAY DIFFRACTION	99.9078

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	0.4066	1.6963	-1.5428	13.3182	-1.1002	10.634	0.053	-0.1028	-0.0538	0.0832	-0.0513	-0.5686	-0.5025	0.6832	-0.0017	0.1333	-0.0107	-0.0367	0.0908	-0.0212	0.0985	13.4956	24.2633	-51.9815
2	2.1055	-2.8248	0.4586	10.7595	0.3083	4.5696	0.0339	0.0614	0.0027	-0.0408	-0.0545	-0.1964	0.0495	0.2127	0.0206	0.0536	-0.0176	-0.0053	0.0644	-0.0058	0.0209	14.0766	16.2017	-54.0648
3	3.4773	2.5115	-3.0113	1.8154	-2.1929	3.2199	0.0193	-0.0312	-0.0813	0.0195	-0.0323	-0.0611	0.0306	0.2124	0.013	0.058	-0.0073	-0.02	0.0657	-0.0073	0.0272	14.6075	4.6456	-59.6669
4	6.366	-3.2951	1.794	4.1265	-1.67	1.2522	0.0144	0.0851	0.0097	0.114	-0.0772	-0.341	-0.0154	0.2357	0.0628	0.0505	0.0028	-0.0113	0.08	-0.0123	0.0513	19.0345	-7.5717	-48.6523
5	0.3646	-0.1106	-0.1687	0.59	0.1126	0.581	-0.0128	-0.1119	0.0302	0.0971	0.0078	-0.0034	-0.0293	0.0281	0.005	0.0565	0.003	-0.0093	0.0504	-0.0136	0.0054	3.0174	8.5175	-34.8893
6	0.6531	-1.8465	0.157	8.9737	-0.5321	0.8213	-0.0651	-0.1856	0.0186	0.2046	0.0944	0.2023	0.0103	-0.0483	-0.0293	0.0693	0.0075	0.0096	0.1189	-0.0222	0.0321	-5.1627	11.5606	-22.3703
7	4.6609	-2.1566	3.0435	6.2155	-5.2392	6.9358	-0.1851	-0.3613	0.3716	0.4466	0.2249	0.1379	-0.2427	-0.2174	-0.0398	0.1602	0.037	-0.0104	0.1535	-0.1018	0.1203	-0.6022	25.0449	-18.2644
8	0.69	-0.0289	0.0315	0.8591	0.1013	1.0763	-0.0105	-0.1574	0.1154	0.1393	0.0268	-0.0455	-0.0806	0.0062	-0.0163	0.0882	0.0027	-0.0047	0.0529	-0.0452	0.0406	1.2298	22.0055	-30.8672
9	5.2751	0.2872	2.7819	6.3135	1.043	4.1131	-0.0204	0.0445	0.2347	-0.1659	-0.0015	-0.385	-0.1587	0.1411	0.0219	0.0564	0.0017	0.0071	0.0582	-0.0264	0.0498	8.3174	21.0164	-35.5132
10	0.9969	-0.4658	0.7294	1.2222	-0.4542	1.6608	-0.0116	-0.0608	0.0749	0.0609	0.0115	-0.0274	-0.0294	-0.0254	0.0001	0.0429	0.0025	0.0012	0.0107	-0.0088	0.0101	1.5479	12.8679	-43.824
11	1.8222	3.9954	1.8434	9.7131	3.2346	2.6412	0.0953	-0.0502	-0.0257	0.3246	-0.1015	-0.1194	0.0558	0.0209	0.0063	0.0904	0.0248	-0.0219	0.0819	-0.0146	0.0107	11.6581	3.8647	-32.3473
12	0.3249	-0.6743	0.3527	2.0629	-1.3669	1.0591	-0.0144	0.0051	0.038	-0.038	0.0061	-0.0805	0.015	-0.0091	0.0083	0.0387	-0.0011	0.0076	0.0238	-0.0043	0.0213	3.3317	10.5398	-52.2211
13	6.4888	-2.5863	-0.3788	2.1118	0.316	2.188	-0.0462	-0.0351	0.373	0.0061	0.0136	-0.0187	-0.3439	-0.0027	0.0326	0.1146	0.0204	-0.0028	0.011	-0.0004	0.0636	-7.3002	29.7205	-52.0589
14	7.8964	1.093	0.5664	1.2744	-0.4704	2.611	0.0731	0.0929	0.3371	-0.0225	0.0471	0.2909	-0.267	-0.3628	-0.1202	0.1649	0.0603	-0.0012	0.0847	-0.0373	0.1718	-18.9774	33.6556	-43.4354
15	5.1672	-1.0639	1.154	3.2164	-0.2549	3.3906	-0.1358	-0.1578	0.441	0.0153	0.069	-0.0566	-0.3393	-0.0455	0.0668	0.1748	0.0061	0	0.0367	-0.0361	0.1215	-3.4778	34.3606	-38.2388
16	6.8202	0.4153	-1.554	1.2663	-0.4201	1.8527	0.1197	-0.1054	0.3236	0.1314	-0.0588	0.2992	-0.1926	-0.2753	-0.061	0.1245	0.0387	0.0143	0.0847	-0.0403	0.1112	-19.3751	27.4746	-40.7616
17	3.9453	0.5273	-0.8978	2.0128	-0.207	2.4032	-0.0016	-0.0077	0.1672	0.0179	0.0094	0.3527	-0.0889	-0.3655	-0.0077	0.0766	0.0238	0.0064	0.073	-0.0172	0.0776	-20.3392	19.1172	-49.1185
18	0.7778	0.1781	0.1431	0.9254	-2.2759	6.4323	-0.0041	-0.1451	0.018	0.0164	0.0234	0.067	0.0694	-0.1355	-0.0193	0.0818	0.0179	0.0279	0.0727	-0.0115	0.078	-17.2331	16.3855	-36.8753
19	1.7068	-0.1208	-0.9535	0.916	0.0007	3.5031	0.0453	-0.0632	0.1459	0.047	-0.0079	0.1337	-0.2921	-0.1105	-0.0373	0.0766	0.03	0.004	0.0309	-0.0229	0.0709	-15.5821	24.3935	-47.553
20	7.9589	2.1325	-3.7489	3.7061	-0.2096	6.3574	0.3481	-0.1673	0.4928	0.0787	-0.1198	0.5068	-0.4627	-0.4354	-0.2283	0.1373	0.0688	0.003	0.1349	-0.0063	0.1733	-24.3991	29.0736	-52.0925

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	3 - 8
2	X-RAY DIFFRACTION	2	ALL	A	9 - 16
3	X-RAY DIFFRACTION	3	ALL	A	17 - 29
4	X-RAY DIFFRACTION	4	ALL	A	30 - 47
5	X-RAY DIFFRACTION	5	ALL	A	48 - 113
6	X-RAY DIFFRACTION	6	ALL	A	114 - 127
7	X-RAY DIFFRACTION	7	ALL	A	128 - 137
8	X-RAY DIFFRACTION	8	ALL	A	138 - 184
9	X-RAY DIFFRACTION	9	ALL	A	185 - 195
10	X-RAY DIFFRACTION	10	ALL	A	196 - 218
11	X-RAY DIFFRACTION	11	ALL	A	219 - 231
12	X-RAY DIFFRACTION	12	ALL	A	232 - 253
13	X-RAY DIFFRACTION	13	ALL	A	254 - 264
14	X-RAY DIFFRACTION	14	ALL	A	265 - 279
15	X-RAY DIFFRACTION	15	ALL	A	280 - 296
16	X-RAY DIFFRACTION	16	ALL	A	297 - 313
17	X-RAY DIFFRACTION	17	ALL	A	314 - 332
18	X-RAY DIFFRACTION	18	ALL	A	333 - 353
19	X-RAY DIFFRACTION	19	ALL	A	354 - 371
20	X-RAY DIFFRACTION	20	ALL	A	372 - 381

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