PDB-8sf4: Cystathionine gamma lyase from Thermobifida fusca in internal ald...

ID or keywords:

Entry

Database: PDB / ID: 8sf4

Title

Cystathionine gamma lyase from Thermobifida fusca in internal aldimine form

Components

Cystathionine gamma-lyase

Keywords

LYASE / PLP / internal aldimine / holoenzyme

Function / homology

Function and homology information

cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding
Similarity search - Function

Biological species

Thermobifida fusca (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.455 Å

Authors

Perkins, L.J. / Buller, A.R. / Bindman, C.A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Multiplexed deconvolution of enzyme function in a PLP-dependent protein family
Authors: Zmich, A.P. / Perkins, L.J. / Bingman, C.A. / Buller, A.R.

History

Deposition	Apr 10, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sf4.cif.gz	160.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8sf4.ent.gz	119.5 KB	Display	PDB format
PDBx/mmJSON format	8sf4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8sf4_validation.pdf.gz	450.8 KB	Display	wwPDB validaton report
Full document	8sf4_full_validation.pdf.gz	453.4 KB	Display
Data in XML	8sf4_validation.xml.gz	20.4 KB	Display
Data in CIF	8sf4_validation.cif.gz	31 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sf/8sf4 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/8sf4	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 gamma-lyase

hetero molecules

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

1

A: Cystathionine gamma-lyase

hetero molecules

A: Cystathionine gamma-lyase

hetero molecules

A: Cystathionine gamma-lyase

hetero molecules

A: Cystathionine gamma-lyase

hetero molecules

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

Unit cell

Length a, b, c (Å)	117.591, 117.591, 117.591
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-87- ARG
2	1	A-770- HOH

#1: Protein	Cystathionine gamma-lyase Mass: 41779.945 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: Q47ST9, cystathionine gamma-lyase
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 389 / 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: 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 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: 1.455→40.003 Å / Num. obs: 94728 / % possible obs: 100 % / Redundancy: 22.1 % / CC_1/2: 1 / R_rim(I) all: 0.075 / Net I/σ(I): 25.36
Reflection shell	Resolution: 1.46→1.49 Å / Redundancy: 21.3 % / Mean I/σ(I) obs: 2.09 / Num. unique obs: 6964 / CC_1/2: 0.748 / R_rim(I) all: 1.697 / % 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: 1.455→40.003 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.979 / SU B: 1.499 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.042
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1481	4687	4.948 %
R_work	0.133	90041	-
all	0.134	-	-
obs	-	94728	99.964 %

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: 20.789 Å²

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

Refinement step

Cycle: LAST / Resolution: 1.455→40.003 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2835	0	24	389	3248

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.013	3021
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	2832
X-RAY DIFFRACTION	r_angle_refined_deg	2.248	1.64	4130
X-RAY DIFFRACTION	r_angle_other_deg	1.679	1.581	6529
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.581	5	402
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.09	20.897	156
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.996	15	457
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.121	15	27
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	390
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	3499
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	645
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	621
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.172	0.2	2631
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	1469
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1348
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	244
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.282	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.038	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.164	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.173	0.2	99
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.231	0.2	24
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.223	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.96	1.281	1563
X-RAY DIFFRACTION	r_mcbond_other	0.943	1.281	1562
X-RAY DIFFRACTION	r_mcangle_it	1.324	1.924	1968
X-RAY DIFFRACTION	r_mcangle_other	1.325	1.925	1969
X-RAY DIFFRACTION	r_scbond_it	1.994	1.532	1457
X-RAY DIFFRACTION	r_scbond_other	1.959	1.532	1457
X-RAY DIFFRACTION	r_scangle_it	2.832	2.199	2158
X-RAY DIFFRACTION	r_scangle_other	2.842	2.203	2159
X-RAY DIFFRACTION	r_lrange_it	5.077	17.486	3439
X-RAY DIFFRACTION	r_lrange_other	4.916	16.532	3349

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.455-1.493	0.234	356	0.231	6609	0.231	6965	0.898	0.887	100	0.207
1.493-1.534	0.205	356	0.185	6383	0.186	6739	0.926	0.928	100	0.159
1.534-1.578	0.185	324	0.168	6264	0.169	6589	0.941	0.944	99.9848	0.138
1.578-1.627	0.174	343	0.152	6038	0.153	6381	0.955	0.955	100	0.124
1.627-1.68	0.169	296	0.14	5966	0.141	6262	0.958	0.966	100	0.111
1.68-1.739	0.161	313	0.134	5681	0.136	5994	0.964	0.971	100	0.105
1.739-1.804	0.144	263	0.125	5533	0.126	5796	0.973	0.976	100	0.098
1.804-1.878	0.145	295	0.128	5289	0.129	5584	0.972	0.974	100	0.103
1.878-1.961	0.161	219	0.118	5140	0.12	5359	0.971	0.98	100	0.096
1.961-2.057	0.14	231	0.125	4889	0.125	5120	0.977	0.979	100	0.105
2.057-2.167	0.155	237	0.123	4652	0.125	4889	0.974	0.978	100	0.107
2.167-2.298	0.143	239	0.121	4382	0.122	4621	0.976	0.98	100	0.107
2.298-2.457	0.132	186	0.116	4183	0.116	4369	0.981	0.981	100	0.105
2.457-2.653	0.131	206	0.116	3853	0.117	4059	0.978	0.98	100	0.109
2.653-2.905	0.135	189	0.123	3562	0.123	3751	0.977	0.979	100	0.121
2.905-3.245	0.164	187	0.138	3246	0.139	3433	0.971	0.976	100	0.14
3.245-3.743	0.139	158	0.136	2842	0.136	3000	0.979	0.981	100	0.146
3.743-4.574	0.121	117	0.115	2472	0.115	2589	0.985	0.985	100	0.132
4.574-6.427	0.154	107	0.148	1919	0.148	2026	0.98	0.98	100	0.173
6.427-40.003	0.147	65	0.171	1138	0.17	1204	0.981	0.974	99.9169	0.212

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	1.01	0.5508	3.257	12.2733	0.7846	10.6032	0.1	-0.2097	-0.0089	0.0851	-0.0371	0.5711	0.395	-0.6782	-0.0629	0.1281	-0.011	0.0457	0.0856	0.0157	0.0769	-13.4365	-24.2779	-52.2422
2	2.309	-3.5785	0.566	10.4858	-0.4552	3.9932	0.0375	0.0705	0.0062	-0.0487	-0.0363	0.1757	-0.0554	-0.1712	-0.0012	0.0492	-0.0189	0.0147	0.0728	0.005	0.0128	-14.0866	-16.1895	-54.3904
3	0.0081	-0.0583	-0.096	2.3777	1.5699	1.6215	-0.0074	0.0232	-0.0025	0.0352	-0.0973	0.2353	0.0037	-0.2621	0.1047	0.0342	-0.0004	0.0084	0.0737	0.0039	0.0357	-16.6609	2.2353	-54.5598
4	0.334	0.1158	0.1289	0.9655	-0.2671	0.9607	-0.0285	-0.0616	-0.002	0.0806	0.0301	0.1285	-0.0002	-0.1198	-0.0016	0.0247	0.0093	0.0174	0.0424	0.0049	0.0209	-9.2323	-5.7659	-41.1018
5	0.6642	-0.5094	-0.4574	2.0207	0.5034	0.9899	-0.0533	-0.1404	-0.0233	0.1689	0.0584	-0.0933	0.0312	0.0864	-0.0051	0.0853	0.0327	-0.0235	0.0889	0.0175	0.0247	5.0828	-13.6181	-24.7044
6	0.3975	-0.0889	-0.1131	0.8825	-0.0923	0.7488	-0.0358	-0.1046	-0.067	0.1261	0.0285	0.0491	0.0836	-0.0219	0.0073	0.0573	0.0069	0.0129	0.0451	0.0186	0.0131	-3.3838	-17.7035	-33.7481
7	0.304	0.0879	-0.0847	4.1217	4.5274	5.085	-0.0147	-0.0164	-0.0037	-0.0197	0.0645	-0.0477	-0.0137	0.0934	-0.0498	0.0083	0.0044	0.0013	0.0366	0.0072	0.0023	-3.5942	-5.0474	-50.1053
8	3.385	-1.0229	0.9006	1.4613	-0.51	1.55	-0.0093	-0.1088	-0.2811	0.0217	0.0469	-0.1103	0.2465	0.181	-0.0377	0.104	0.034	0.0139	0.0528	0.0042	0.062	9.4939	-28.8113	-50.1188
9	1.4688	0.251	-0.5987	1.413	-0.3765	1.7664	-0.0451	-0.1374	-0.2004	0.0686	-0.0257	-0.2022	0.2135	0.2863	0.0707	0.105	0.0596	-0.0092	0.0793	0.0095	0.0662	14.6919	-26.9366	-43.2822
10	1.0402	0.0752	0.3755	0.937	0.5135	4.1615	0.0203	-0.109	-0.0796	0.082	0.0236	-0.1881	0.0628	0.3375	-0.0439	0.0728	0.0246	-0.0067	0.0855	0.0178	0.0742	18.1954	-22.2595	-44.4246

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 - 42
4	X-RAY DIFFRACTION	4	ALL	A	43 - 90
5	X-RAY DIFFRACTION	5	ALL	A	91 - 132
6	X-RAY DIFFRACTION	6	ALL	A	133 - 230
7	X-RAY DIFFRACTION	7	ALL	A	231 - 246
8	X-RAY DIFFRACTION	8	ALL	A	247 - 276
9	X-RAY DIFFRACTION	9	ALL	A	277 - 332
10	X-RAY DIFFRACTION	10	ALL	A	333 - 381

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