PDB-8sf5: Promiscuous amino acid gamma synthase from Caldicellulosiruptor h...

ID or keywords:

Entry

Database: PDB / ID: 8sf5

Title

Promiscuous amino acid gamma synthase from Caldicellulosiruptor hydrothermalis in open conformation

Components

O-acetylhomoserine/O-acetylserine sulfhydrylase

Keywords

TRANSFERASE / Pyridoxal Phosphate / Amino acid synthase

Function / homology

Function and homology information

O-acetylhomoserine aminocarboxypropyltransferase activity / L-homocysteine biosynthetic process / cysteine synthase / cysteine synthase activity / transsulfuration / cysteine biosynthetic process from serine / pyridoxal phosphate binding / cytoplasm
Similarity search - Function

Biological species

Caldicellulosiruptor hydrothermalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Buller, A.R. / Zmich, A.P. / Bingman, C.A.

Funding support

United States, 1items

Citation

Journal: Acs Catalysis / Year: 2023
Title: Multiplexed Assessment of Promiscuous Non-Canonical Amino Acid Synthase Activity in a Pyridoxal Phosphate-Dependent Protein Family.
Authors: Zmich, A. / Perkins, L.J. / Bingman, C. / Acheson, J.F. / Buller, A.R.

History

Deposition	Apr 10, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 27, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sf5.cif.gz	304.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8sf5.ent.gz	238.5 KB	Display	PDB format
PDBx/mmJSON format	8sf5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8sf5_validation.pdf.gz	438.6 KB	Display	wwPDB validaton report
Full document	8sf5_full_validation.pdf.gz	442.7 KB	Display
Data in XML	8sf5_validation.xml.gz	28.2 KB	Display
Data in CIF	8sf5_validation.cif.gz	38.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sf/8sf5 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/8sf5	HTTPS FTP

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Related structure data

Related structure data	8sf6C C: citing same article (ref.)
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: O-acetylhomoserine/O-acetylserine sulfhydrylase

B: O-acetylhomoserine/O-acetylserine sulfhydrylase

96.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: O-acetylhomoserine/O-acetylserine sulfhydrylase

B: O-acetylhomoserine/O-acetylserine sulfhydrylase

A: O-acetylhomoserine/O-acetylserine sulfhydrylase

B: O-acetylhomoserine/O-acetylserine sulfhydrylase

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

Unit cell

Length a, b, c (Å)	79.921, 79.921, 230.492
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	O-acetylhomoserine/O-acetylserine sulfhydrylase Mass: 48327.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldicellulosiruptor hydrothermalis (bacteria) Gene: Calhy_1610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E4QC33
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.37 Å³/Da / Density % sol: 48.05 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 16% PEG 3350, 0.125 M Sodium Thiocyanate pH 8.0. Protein was 20 mg/mL in 50 mM HEPES pH 7.5. Four microliter drops were formed with a 1:1 mixture of protein and well solution. Crystals ...Details: 16% PEG 3350, 0.125 M Sodium Thiocyanate pH 8.0. Protein was 20 mg/mL in 50 mM HEPES pH 7.5. Four microliter drops were formed with a 1:1 mixture of protein and well solution. Crystals formed slowly over the course of 10 months

Crystal

Density Matthews: 2.37 Å³/Da / Density % sol: 48.05 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 3350, 0.125 M Sodium Thiocyanate pH 8.0. Protein was 20 mg/mL in 50 mM HEPES pH 7.5. Four microliter drops were formed with a 1:1 mixture of protein and well solution. Crystals ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.3→45 Å / Num. obs: 38922 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC_1/2: 0.999 / R_rim(I) all: 0.126 / Net I/σ(I): 13.6
Reflection shell	Resolution: 2.3→2.36 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 1.29 / Num. unique obs: 2810 / CC_1/2: 0.473 / R_rim(I) all: 1.949 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→44.324 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.946 / SU B: 23.443 / SU ML: 0.241 / Cross valid method: FREE R-VALUE / ESU R: 0.347 / ESU R Free: 0.233
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.243	2006	5.157 %
R_work	0.2073	36892	-
all	0.209	-	-
obs	-	38898	99.915 %

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: 58.219 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.698 Å²	0.349 Å²	-0 Å²
2-	-	0.698 Å²	0 Å²
3-	-	-	-2.264 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→44.324 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6149	0	0	30	6179

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	6307
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	5876
X-RAY DIFFRACTION	r_angle_refined_deg	1.305	1.638	8607
X-RAY DIFFRACTION	r_angle_other_deg	1.165	1.572	13478
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.71	5	808
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.508	23.152	276
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.486	15	936
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.27	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	867
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	7208
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1408
X-RAY DIFFRACTION	r_nbd_refined	0.181	0.2	1136
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.172	0.2	5327
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	3074
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	2690
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	137
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.174	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	112
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.172	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	0.957	3.637	3241
X-RAY DIFFRACTION	r_mcbond_other	0.957	3.636	3240
X-RAY DIFFRACTION	r_mcangle_it	1.561	5.451	4046
X-RAY DIFFRACTION	r_mcangle_other	1.561	5.452	4047
X-RAY DIFFRACTION	r_scbond_it	1.032	3.74	3066
X-RAY DIFFRACTION	r_scbond_other	1.032	3.74	3067
X-RAY DIFFRACTION	r_scangle_it	1.702	5.574	4561
X-RAY DIFFRACTION	r_scangle_other	1.702	5.574	4561
X-RAY DIFFRACTION	r_lrange_it	2.95	42.64	6657
X-RAY DIFFRACTION	r_lrange_other	2.949	42.631	6655

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 (%)
2.3-2.36	0.403	102	0.347	2700	X-RAY DIFFRACTION	99.8575
2.36-2.424	0.364	203	0.321	2567	X-RAY DIFFRACTION	99.9639
2.424-2.494	0.317	101	0.307	2559	X-RAY DIFFRACTION	99.9624
2.494-2.571	0.35	164	0.299	2432	X-RAY DIFFRACTION	100
2.571-2.655	0.298	140	0.259	2406	X-RAY DIFFRACTION	100
2.655-2.747	0.254	100	0.251	2345	X-RAY DIFFRACTION	100
2.747-2.851	0.309	100	0.234	2247	X-RAY DIFFRACTION	100
2.851-2.967	0.296	102	0.22	2179	X-RAY DIFFRACTION	100
2.967-3.098	0.25	204	0.222	1993	X-RAY DIFFRACTION	99.9545
3.098-3.248	0.322	100	0.218	1985	X-RAY DIFFRACTION	100
3.248-3.423	0.258	103	0.223	1905	X-RAY DIFFRACTION	100
3.423-3.629	0.237	98	0.192	1836	X-RAY DIFFRACTION	100
3.629-3.878	0.179	100	0.171	1677	X-RAY DIFFRACTION	99.9438
3.878-4.186		0	0.157	1698	X-RAY DIFFRACTION	100
4.186-4.582	0.212	101	0.156	1440	X-RAY DIFFRACTION	100
4.582-5.116	0.187	97	0.158	1331	X-RAY DIFFRACTION	100
5.116-5.895	0.274	93	0.198	1169	X-RAY DIFFRACTION	100
5.895-7.189		0	0.227	1093	X-RAY DIFFRACTION	99.8174
7.189-10.04	0.196	98	0.17	780	X-RAY DIFFRACTION	99.7727
10.04-44.3		0	0.239	535	X-RAY DIFFRACTION	98.8909

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	1.6074	-0.2466	0.0615	3.0457	-0.1142	0.4266	-0.1002	-0.3335	-0.4746	0.2305	0.0741	0.4029	-0.0202	-0.0815	0.0261	0.2026	0.0656	0.0745	0.1897	0.0309	0.2305	-28.356	21.398	42.896
2	23.8658	4.536	10.4939	2.4967	-1.0916	10.4513	0.23	0.288	-0.4845	0.1224	-0.2673	-0.1884	-0.0778	0.7511	0.0372	0.4716	0.1141	-0.0002	0.4488	-0.1027	0.5602	-33.219	0.083	35.426
3	2.0952	0.596	1.2375	0.249	0.6094	3.2935	0.0084	0.0839	-0.126	-0.0942	0.0428	-0.047	0.0717	-0.0577	-0.0512	0.2425	-0.0076	0.0422	0.0643	-0.0042	0.0739	-31.248	20.951	22.616
4	7.612	-1.7131	0.2003	6.7192	-0.1738	1.2074	-0.1506	0.6208	0.3726	-0.5288	0.0551	-0.1746	-0.1438	-0.0848	0.0955	0.3755	-0.0953	0.0264	0.3013	0.0125	0.0297	-30.87	26.882	5.427
5	1.2272	0.4624	0.5051	2.1312	0.2802	1.8656	-0.1484	0.1819	0.1229	-0.2675	0.0656	0.1413	-0.1396	-0.1514	0.0828	0.1979	0.0167	-0.0007	0.1197	0.0233	0.0581	-33.748	31.357	18.998
6	7.6699	-1.9471	1.4637	9.223	-1.1138	3.5193	0.0055	0.2291	-0.4611	-0.5679	0.2212	0.0125	0.48	-0.1487	-0.2267	0.3087	-0.0502	0.0276	0.2488	-0.0999	0.1525	-43.552	11.281	17.192
7	10.8135	-1.4466	-1.1569	5.139	0.5241	2.0472	-0.1306	-0.3326	-0.6942	-0.152	0.1102	0.0761	0.1674	-0.0809	0.0204	0.1941	-0.0152	0.0288	0.1362	0.005	0.0981	-37.102	12.318	23.852
8	0.9002	-0.0562	-0.1513	2.1391	-0.1214	1.6681	-0.0604	0.1545	0.1909	-0.0288	0.0141	0.1215	-0.3502	-0.0964	0.0462	0.1239	0.0416	-0.0054	0.0813	0.0433	0.0869	-25.298	42.106	24
9	2.6759	-0.2869	0.0896	2.6334	-0.6544	3.8855	-0.1837	0.3361	-0.0643	-0.426	0.0355	-0.1458	0.0716	0.3965	0.1483	0.2816	-0.0019	0.0036	0.1536	0.0449	0.0598	-13.949	44.397	17.131
10	2.3729	0.7345	-0.396	2.4991	-0.9897	5.8043	-0.2004	0.4114	0.1135	-0.3537	0.1658	-0.0891	-0.2536	0.1036	0.0346	0.2044	0.0067	0.0129	0.1346	0.0741	0.1191	-15.085	46.911	15.403
11	3.3143	3.5289	-2.8903	6.8088	-3.1075	3.9688	-0.1402	0.0848	-0.5121	0.1788	-0.1456	-0.3522	0.0234	0.5525	0.2858	0.3184	0.0171	0.246	0.3216	0.0047	0.5046	5.95	9.988	27.596
12	8.5957	-1.6091	4.2086	4.5991	-1.6125	3.7577	0.1899	0.539	-0.1342	-0.473	-0.2483	-0.2337	0.0065	0.3822	0.0584	0.1684	0.0237	0.1032	0.064	-0.0093	0.1277	-2.744	26.868	27.655
13	3.2084	1.2476	0.5254	1.2433	0.3651	2.0797	-0.3148	0.2895	-0.6559	-0.317	0.18	-0.2127	0.1906	-0.157	0.1348	0.3432	-0.0275	0.2165	0.1028	-0.0964	0.2949	-17.386	3.906	14.217
14	1.9797	0.6305	0.6761	1.1439	0.4079	1.9303	-0.363	0.3167	-0.8643	-0.2744	0.1893	-0.3478	0.2293	-0.0207	0.1737	0.3716	-0.0521	0.3457	0.0995	-0.1693	0.5577	-10.964	-1.146	15.574
15	6.0832	-2.1546	-4.8042	14.0228	0.538	3.91	-0.0022	0.5812	-0.1162	0.473	-0.1432	0.2194	-0.0763	-0.4601	0.1454	0.5686	-0.0987	-0.0044	0.7447	-0.1532	0.3359	-12.568	15.983	-0.48
16	2.4719	-0.2323	0.5096	0.4767	0.5612	1.805	-0.2075	0.3339	-0.3195	-0.3026	0.0706	-0.1321	-0.2231	-0.0136	0.1369	0.3857	-0.1414	0.2333	0.1458	-0.1189	0.3305	-9.338	15.17	17.967
17	0.5909	1.0657	-0.0924	2.5407	-1.1758	1.8703	0.1212	-0.1325	-0.3174	0.0253	-0.2489	-0.364	0.5319	0.0226	0.1277	0.5571	0.095	0.447	0.151	0.0953	1.0993	-11.19	-15.334	34.052
18	1.7078	-0.3156	-1.6204	2.7226	1.5663	3.9354	-0.0586	0.1125	-0.8052	-0.2583	-0.0817	-0.1115	0.1031	-0.3298	0.1403	0.3393	0.0604	0.2379	0.1192	0.0442	0.7374	-17.484	-10.26	34.119
19	4.7224	4.5809	4.1879	19.4042	6.8311	4.5312	-0.3643	0.5494	0.2502	-0.7634	0.2571	0.7276	-0.0941	0.1113	0.1073	0.683	-0.0929	0.0052	0.847	0.0373	0.9483	-32.762	-10.241	26.905
20	6.4436	4.3377	-0.9258	5.4133	0.8879	4.7128	0.0328	-0.3422	-0.5932	-0.0954	-0.426	-0.3624	0.5341	-0.228	0.3931	0.2993	0.0543	0.2638	0.0686	0.091	0.657	-17.609	-13.136	41.615

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	5 - 37
2	X-RAY DIFFRACTION	2	ALL	A	38 - 50
3	X-RAY DIFFRACTION	3	ALL	A	60 - 109
4	X-RAY DIFFRACTION	4	ALL	A	110 - 147
5	X-RAY DIFFRACTION	5	ALL	A	148 - 226
6	X-RAY DIFFRACTION	6	ALL	A	227 - 248
7	X-RAY DIFFRACTION	7	ALL	A	249 - 268
8	X-RAY DIFFRACTION	8	ALL	A	269 - 333
9	X-RAY DIFFRACTION	9	ALL	A	334 - 385
10	X-RAY DIFFRACTION	10	ALL	A	386 - 423
11	X-RAY DIFFRACTION	11	ALL	B	5 - 20
12	X-RAY DIFFRACTION	12	ALL	B	21 - 61
13	X-RAY DIFFRACTION	13	ALL	B	62 - 143
14	X-RAY DIFFRACTION	14	ALL	B	144 - 232
15	X-RAY DIFFRACTION	15	ALL	B	233 - 247
16	X-RAY DIFFRACTION	16	ALL	B	248 - 289
17	X-RAY DIFFRACTION	17	ALL	B	290 - 326
18	X-RAY DIFFRACTION	18	ALL	B	327 - 380
19	X-RAY DIFFRACTION	19	ALL	B	381 - 398
20	X-RAY DIFFRACTION	20	ALL	B	399 - 427

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