PDB-5dw0: TrpB from Pyrococcus furiosus with L-serine bound as the external...

ID or keywords:

Entry

Database: PDB / ID: 5dw0

Title

TrpB from Pyrococcus furiosus with L-serine bound as the external aldimine

Components

Tryptophan synthase beta chain 1

Keywords

LYASE / PLP / External Aldimine / Pr

Function / homology

Function and homology information

tryptophan synthase /

tryptophan synthase activity /

cytoplasm
Similarity search - Function

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.01 Å

Authors

Buller, A.R. / Arnold, F.H.

Funding support

United States, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Directed evolution of the tryptophan synthase beta-subunit for stand-alone function recapitulates allosteric activation.
Authors: Buller, A.R. / Brinkmann-Chen, S. / Romney, D.K. / Herger, M. / Murciano-Calles, J. / Arnold, F.H.

History

Deposition	Sep 22, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 3, 2016	Group: Database references
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5dw0.cif.gz	585.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5dw0.ent.gz	485.7 KB	Display	PDB format
PDBx/mmJSON format	5dw0.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/dw/5dw0 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dw0	HTTPS FTP

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Related structure data

Related structure data	5dvzC 5dw3C 5e0kC C: citing same article (ref.)
Similar structure data	6ami-1 5vm5-1 6cuv-2 5dvz-1 6amh-2 5t6m-1 5t6m-2 6am9-1 6cuz-2 6am8-1 6am8-2 6ami-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (9)

Deposited unit

A: Tryptophan synthase beta chain 1

B: Tryptophan synthase beta chain 1

C: Tryptophan synthase beta chain 1

D: Tryptophan synthase beta chain 1

hetero molecules

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

1

A: Tryptophan synthase beta chain 1

B: Tryptophan synthase beta chain 1

hetero molecules

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

2

C: Tryptophan synthase beta chain 1

D: Tryptophan synthase beta chain 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	84.241, 109.131, 160.797
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Tryptophan synthase beta chain 1 Mass: 43656.926 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical	ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE Mass: 336.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₇N₂O₈P
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 41.88 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 25% PEG3350 100 mM HEPES pH 7.85

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9785 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 2.01→40 Å / Num. obs: 91540 / % possible obs: 98 % / Redundancy: 9.8 % / Net I/σ(I): 15.1
Reflection shell	Resolution: 2.01→2.05 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 0.9 / % possible all: 67.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Resolution: 2.01→40 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.952 / SU B: 12.864 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22123	4812	5 %	RANDOM
R_work	0.17577	-	-	-
obs	0.17805	91540	97.75 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 42.654 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.48 Å²	-0 Å²	0 Å²
2-	-	0.63 Å²	0 Å²
3-	-	-	-3.1 Å²

Refinement step

Cycle: 1 / Resolution: 2.01→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11661	0	92	216	11969

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	12002
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11488
X-RAY DIFFRACTION	r_angle_refined_deg	1.413	1.97	16260
X-RAY DIFFRACTION	r_angle_other_deg	0.731	3	26339
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.01	5	1541
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.38	23.923	492
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.238	15	1948
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.443	15	61
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1796
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	13717
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2706
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.126	1.757	6182
X-RAY DIFFRACTION	r_mcbond_other	1.126	1.756	6181
X-RAY DIFFRACTION	r_mcangle_it	1.748	2.626	7714
X-RAY DIFFRACTION	r_mcangle_other	1.748	2.627	7715
X-RAY DIFFRACTION	r_scbond_it	1.843	2.041	5820
X-RAY DIFFRACTION	r_scbond_other	1.842	2.041	5820
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.984	2.959	8546
X-RAY DIFFRACTION	r_long_range_B_refined	5.391	14.835	13630
X-RAY DIFFRACTION	r_long_range_B_other	5.382	14.776	13597
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.015→2.067 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.368	276	-
R_work	0.367	5105	-
obs	-	-	74.81 %

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	0.6715	-0.1252	-0.3287	1.1818	0.4069	1.5998	-0.0274	-0.1416	0.0037	0.025	0.0394	-0.0931	0.2385	0.2856	-0.012	0.1324	0.0328	-0.0064	0.2984	0.0086	0.2522	9.4057	-42.3635	-14.7781
2	2.3769	-0.7012	-1.4471	2.2854	0.3408	3.6538	-0.0205	-0.0538	0.1018	-0.0273	-0.0366	0.1107	0.1517	-0.3007	0.0571	0.1755	-0.0381	-0.0174	0.2471	-0.0067	0.2227	-8.2981	-47.9955	-16.0304
3	0.7037	-0.1945	-0.0736	1.4037	0.1255	1.7902	0.0143	-0.1985	0.1037	0.1108	0.0236	-0.1333	0.0643	0.315	-0.0378	0.1208	0.0156	-0.0205	0.3181	-0.0145	0.2334	8.6301	-37.1622	-10.2852
4	3.1171	-3.0378	1.0199	3.8064	-1.7046	3.8575	-0.0055	-0.2943	-0.0097	0.1804	0.0942	0.1809	-0.1729	-0.1942	-0.0887	0.1982	0.0089	0.0043	0.2922	-0.0257	0.1938	-6.0038	-32.0015	0.6191
5	1.7235	-0.0158	0.4272	0.9073	-0.4966	3.5996	0.1104	-0.304	0.0882	0.155	0.0371	-0.006	-0.1175	-0.1342	-0.1475	0.1585	0.0059	0.0155	0.2408	-0.0556	0.2229	-3.1313	-29.0021	-6.3928
6	0.6262	0.1067	-0.5958	2.4824	-0.1153	5.0614	0.0922	-0.0379	0.1902	-0.0579	0.007	-0.128	-0.5209	-0.1855	-0.0993	0.2119	0.0314	0.0314	0.2424	-0.0097	0.2795	-1.0137	-22.6425	-21.4973
7	2.8847	-0.3508	0.7374	1.6798	-0.3424	1.7002	0.1223	0.0088	0.2126	-0.06	-0.0386	-0.0171	-0.2085	0.0338	-0.0837	0.2653	0.0013	0.0562	0.2735	-0.0144	0.2354	-2.2029	-24.8885	-22.0718
8	0.8742	0.7892	0.2712	0.7696	-0.0281	2.9949	-0.2119	0.2051	0.0707	-0.3272	0.1627	0.0042	-0.1693	0.0027	0.0491	0.6574	0.1007	0.1863	0.215	0.0937	0.1428	4.2087	-26.8096	-62.8588
9	0.4263	-0.2373	-0.094	1.0188	0.151	1.7985	0.0524	0.0254	0.0843	-0.1793	-0.0502	-0.1593	-0.1801	0.0953	-0.0022	0.2052	0.0096	0.0576	0.2131	0.0278	0.2354	5.3072	-32.6893	-40.4458
10	5.3686	4.3717	-0.4604	11.1113	4.2613	6.2543	-0.0276	0.0248	-0.1203	-0.0873	-0.23	0.4547	0.2461	-0.5868	0.2576	0.2278	0.091	0.0045	0.3023	0.017	0.2264	-12.1469	-30.7384	-36.1113
11	0.3955	-0.1337	-0.0855	1.4485	-0.0909	1.6437	0.0708	0.0738	0.0298	-0.3864	-0.0983	-0.0531	-0.071	0.0115	0.0274	0.2793	0.0428	0.0474	0.2128	0.016	0.2062	3.6384	-36.7303	-50.0472
12	3.6273	1.7075	-0.7534	2.2521	-1.744	1.7267	-0.0983	0.1801	-0.1757	-0.4124	0.0782	-0.0324	0.2864	-0.3238	0.0201	0.4417	0.0289	-0.0229	0.3719	-0.0404	0.0778	-6.5769	-44.6023	-60.2469
13	1.1368	-0.1685	-0.4073	1.6518	-0.1283	2.1245	0.0478	0.1045	-0.0707	-0.3016	-0.0571	0.0381	0.2464	-0.166	0.0092	0.3148	0.0044	0.0097	0.2101	-0.0236	0.1983	-0.5582	-50.3428	-46.9959
14	15.6145	1.0235	0.9629	7.5708	-2.0114	8.0447	0.2179	0.113	-0.8202	0.1603	0.2171	0.3801	0.041	-1.1245	-0.435	0.2145	0.0062	0.0203	0.3691	0.0043	0.2504	-12.2029	-45.9516	-34.0406
15	1.8158	-0.3682	0.4071	0.3059	-0.4132	3.8845	-0.0847	-0.2684	0.0258	0.1258	0.2075	0.1857	-0.2703	-0.6233	-0.1228	0.1217	0.0653	0.0489	0.323	0.0641	0.2103	27.231	-10.7016	-26.7898
16	0.5138	0.1267	0.2515	0.6847	-0.3732	1.7931	0.0087	-0.019	0.0316	-0.0759	0.0768	0.009	0.0871	-0.1668	-0.0855	0.1506	-0.0104	-0.0013	0.2362	0.0248	0.251	38.0805	-14.7273	-40.543
17	1.9793	-0.2265	0.9011	2.0449	-0.5343	4.5802	-0.0602	-0.0878	0.0532	0.2947	-0.0337	-0.1067	-0.1233	0.4655	0.0939	0.2159	-0.0143	0.0044	0.2352	0.0112	0.2303	49.6601	-2.8674	-33.4487
18	0.8391	-0.3168	-0.1178	1.1393	-0.3047	2.1146	-0.0329	-0.1001	-0.0939	0.0471	0.1188	0.1637	0.3096	-0.3541	-0.0859	0.1737	-0.0411	0.0094	0.2468	0.0499	0.2397	34.2679	-21.1915	-31.4903
19	7.4803	-3.108	-3.583	1.5276	2.1102	3.5372	-0.0524	-0.4673	0.0229	0.1035	0.144	-0.0641	0.1794	0.2631	-0.0916	0.2335	0.0378	-0.021	0.2718	0.0298	0.1953	50.7628	-20.362	-20.4893
20	1.3853	0.1714	-0.3757	1.0136	-0.2753	3.0751	0.052	-0.1339	-0.0175	0.0238	-0.0025	0.0101	0.3081	0.2992	-0.0495	0.2399	0.0689	-0.0217	0.2186	0.0188	0.2314	49.6419	-24.5223	-31.5915
21	2.4312	0.3969	-0.9875	3.6589	0.183	1.7917	0.0651	0.0413	-0.1156	0.1668	-0.0546	-0.1313	0.3059	0.1729	-0.0105	0.3188	0.0368	-0.0587	0.2779	0.0192	0.2015	48.8859	-28.915	-41.456
22	0.6066	0.7604	-1.0952	3.0422	0.7016	5.0723	-0.3744	0.1352	-0.1858	-1.1413	-0.0042	-0.0191	0.7968	-0.1179	0.3786	0.9481	0.1509	-0.0897	0.2562	-0.0904	0.1294	43.9548	-26.8186	-82.6515
23	0.8481	-0.2746	-0.0514	0.9291	0.0187	1.6218	-0.0058	0.0815	-0.0283	-0.1226	0.041	0.0693	0.3572	-0.1649	-0.0352	0.2877	-0.0238	-0.0498	0.2314	0.0002	0.2128	38.6375	-21.4509	-60.4405
24	1.9329	-0.162	-0.0529	4.9374	-2.2705	4.684	-0.0633	0.0253	0.0787	-0.0543	0.0488	-0.1021	-0.1732	0.5375	0.0145	0.2575	0.0893	-0.0272	0.3248	-0.0077	0.1815	57.8249	-19.7264	-59.821
25	0.9247	-0.282	0.0789	0.9529	-0.1212	1.8873	0.0403	0.1831	0.0189	-0.2402	-0.0307	0.0382	0.2392	0.0045	-0.0096	0.2744	0.0005	-0.047	0.2573	0.0078	0.1667	40.7856	-17.1986	-70.7121
26	0.2429	1.0405	0.1106	9.1825	5.0532	5.6052	-0.0371	0.0854	0.0429	-0.2866	0.266	-0.2641	-0.2452	0.4765	-0.2289	0.3056	-0.0377	-0.0049	0.3095	0.0728	0.1608	48.5441	-5.0742	-79.5529
27	1.1546	-0.04	0.1175	1.2692	0.1994	3.5896	0.0281	0.1301	0.1265	-0.3175	0.0504	-0.014	-0.1836	0.1702	-0.0785	0.2339	-0.0003	-0.0113	0.215	0.0583	0.2369	42.5652	-3.6153	-68.222
28	3.1702	-0.3658	1.2486	1.9671	0.0249	3.2094	-0.0359	0.0153	0.2951	0.0087	0.0091	0.0051	-0.2895	0.0257	0.0268	0.2324	-0.008	-0.0064	0.2322	0.0409	0.2081	37.682	-2.0352	-59.1187

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 104
2	X-RAY DIFFRACTION	2	A	105 - 166
3	X-RAY DIFFRACTION	3	A	167 - 254
4	X-RAY DIFFRACTION	4	A	255 - 283
5	X-RAY DIFFRACTION	5	A	284 - 332
6	X-RAY DIFFRACTION	6	A	333 - 357
7	X-RAY DIFFRACTION	7	A	358 - 388
8	X-RAY DIFFRACTION	8	B	1 - 27
9	X-RAY DIFFRACTION	9	B	28 - 134
10	X-RAY DIFFRACTION	10	B	135 - 149
11	X-RAY DIFFRACTION	11	B	150 - 255
12	X-RAY DIFFRACTION	12	B	256 - 281
13	X-RAY DIFFRACTION	13	B	282 - 374
14	X-RAY DIFFRACTION	14	B	375 - 385
15	X-RAY DIFFRACTION	15	C	1 - 44
16	X-RAY DIFFRACTION	16	C	45 - 132
17	X-RAY DIFFRACTION	17	C	133 - 170
18	X-RAY DIFFRACTION	18	C	171 - 251
19	X-RAY DIFFRACTION	19	C	252 - 281
20	X-RAY DIFFRACTION	20	C	282 - 354
21	X-RAY DIFFRACTION	21	C	355 - 385
22	X-RAY DIFFRACTION	22	D	1 - 29
23	X-RAY DIFFRACTION	23	D	30 - 121
24	X-RAY DIFFRACTION	24	D	122 - 150
25	X-RAY DIFFRACTION	25	D	151 - 254
26	X-RAY DIFFRACTION	26	D	255 - 283
27	X-RAY DIFFRACTION	27	D	284 - 352
28	X-RAY DIFFRACTION	28	D	353 - 385

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