PDB-5dw3: Tryptophan Synthase beta-subunit from Pyrococcus furiosus with pr...

ID or keywords:

Entry

Database: PDB / ID: 5dw3

Title

Tryptophan Synthase beta-subunit from Pyrococcus furiosus with product L-tryptophan non-covalently bound in the active site

Components

Tryptophan synthase beta chain 1

Keywords

LYASE / Tryptophan synthase / PLP / External Aldimine / Substrate Bound

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: 1.74 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5dw3.cif.gz	592.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5dw3.ent.gz	505.9 KB	Display	PDB format
PDBx/mmJSON format	5dw3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5dw3_validation.pdf.gz	496.5 KB	Display	wwPDB validaton report
Full document	5dw3_full_validation.pdf.gz	516.4 KB	Display
Data in XML	5dw3_validation.xml.gz	57.6 KB	Display
Data in CIF	5dw3_validation.cif.gz	79.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dw/5dw3 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dw3	HTTPS FTP

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Related structure data

Related structure data	5dvzC 5dw0C 5e0kC C: citing same article (ref.)
Similar structure data	6am9-1 5dw0-1 6ami-1 6cuv-1 5vm5-1 5ixj-2 5t6m-1 5t6m-2 6am8-2 6cuv-2 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 (10)

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

177 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
88.2 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
88.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	83.738, 108.931, 160.106
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: 43885.047 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-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-TRP / TRYPTOPHAN Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.13 Å³/Da / Density % sol: 42.29 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 25% PEG3350 0.1 M 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: 0.9795 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.74→80 Å / Num. obs: 140124 / % possible obs: 98.7 % / Redundancy: 9.8 % / Net I/σ(I): 18
Reflection shell	Resolution: 1.74→1.77 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1 / % possible all: 75

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0107	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Resolution: 1.74→40 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.952 / SU B: 7.496 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22421	7347	5 %	RANDOM
R_work	0.18467	-	-	-
obs	0.18666	140124	98.42 %	-

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: 40.797 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.07 Å²	0 Å²	0 Å²
2-	-	1.85 Å²	-0 Å²
3-	-	-	-3.91 Å²

Refinement step

Cycle: LAST / Resolution: 1.74→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11658	0	74	301	12033

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	12004
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11432
X-RAY DIFFRACTION	r_angle_refined_deg	1.882	1.97	16268
X-RAY DIFFRACTION	r_angle_other_deg	0.947	3	26216
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.532	5	1537
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.605	24	495
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.559	15	1928
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.874	15	59
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	1788
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.021	13698
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2701
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	1.457	1.747	6163
X-RAY DIFFRACTION	r_mcbond_other	1.457	1.747	6162
X-RAY DIFFRACTION	r_mcangle_it	2.077	2.608	7686
X-RAY DIFFRACTION	r_mcangle_other	2.077	2.608	7687
X-RAY DIFFRACTION	r_scbond_it	2.166	1.987	5841
X-RAY DIFFRACTION	r_scbond_other	2.162	1.983	5833
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.277	2.876	8567
X-RAY DIFFRACTION	r_long_range_B_refined	5.626	14.683	13745
X-RAY DIFFRACTION	r_long_range_B_other	5.616	14.527	13650
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.742→1.787 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.376	436	-
R_work	0.359	8315	-
obs	-	-	79.91 %

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	0.3865	0.1367	0.0056	0.9953	-0.2723	1.7439	0.0188	0.0923	0.0331	-0.1167	0.0137	0.0134	-0.2667	0.2504	-0.0325	0.2021	-0.0487	0.0426	0.1512	0.009	0.2485	92.044	21.7685	194.6153
2	1.6975	0.4911	0.1451	2.1367	-0.1182	3.9262	0.0014	0.0241	-0.083	-0.1258	-0.0331	0.1266	-0.2522	-0.356	0.0318	0.241	0.069	0.0245	0.1472	0.0299	0.2242	75.5516	25.3992	199.1312
3	0.6431	-0.1017	0.1558	1.3355	-0.2724	1.7616	-0.0093	0.1423	-0.0071	-0.2435	0.0185	0.0205	-0.1615	0.0809	-0.0091	0.208	-0.0085	0.0284	0.1287	0.01	0.2142	87.5059	18.3146	190.851
4	2.7994	1.7075	-1.4349	3.2866	-3.1754	4.7957	0.0017	0.2027	-0.1255	-0.3127	0.1266	0.2402	0.3506	-0.3059	-0.1283	0.25	-0.0541	-0.067	0.1895	-0.029	0.1531	76.8644	9.1587	180.9411
5	5.0804	-3.9659	11.1561	17.434	-13.5257	26.1633	-0.1955	-0.6556	-0.0524	-0.9351	0.5313	0.9363	-0.1773	-1.4653	-0.3358	0.3649	0.1249	-0.2364	0.5535	0.105	0.2359	69.4882	11.9353	177.8718
6	0.9395	0.1003	-0.1396	0.8613	-0.1766	3.025	0.0501	0.1077	-0.0696	-0.2249	0.0226	0.0615	0.3176	-0.1049	-0.0728	0.2028	-0.0138	-0.0177	0.1165	-0.0246	0.2366	82.8546	4.8077	193.8847
7	1.6295	-0.3171	0.4678	1.7662	-0.6377	2.6997	0.0622	-0.0537	-0.2064	-0.1775	0.0293	0.1706	0.2906	-0.1369	-0.0915	0.1658	-0.0394	0.0054	0.1147	-0.009	0.2584	85.1612	2.8733	200.737
8	0.8372	0.0096	-0.2824	0.9167	0.2264	1.8325	0.0396	-0.133	-0.0092	0.0514	0.0402	-0.1216	0.0297	0.3386	-0.0799	0.1092	-0.0149	-0.0034	0.2002	-0.0044	0.2833	93.6167	14.3707	226.0008
9	2.156	-0.2718	-0.0971	1.1794	-0.2386	2.6224	-0.0601	-0.0733	-0.1313	0.0382	0.0057	-0.0528	0.4028	0.177	0.0544	0.155	0.0122	0.0099	0.1005	-0.0003	0.242	87.6906	3.2954	226.0588
10	1.4607	-0.0352	-1.0586	1.042	0.2036	3.5541	-0.0204	-0.0299	0.0517	0.0838	-0.0593	0.0825	0.2365	-0.4134	0.0797	0.1225	-0.0648	0.0009	0.1828	-0.0096	0.2456	75.1653	6.1035	224.1297
11	1.3747	0.3116	-0.171	2.2364	0.0344	1.8813	-0.0436	-0.1295	0.0084	0.1438	0.0954	-0.0968	0.2231	0.2301	-0.0517	0.1453	0.005	-0.0247	0.2193	-0.002	0.2688	91.5335	10.9761	230.1489
12	0.5636	-0.3143	-0.1454	1.2577	-0.1634	3.0504	0.031	-0.224	0.0586	0.1959	0.0824	0.0144	-0.2203	-0.1632	-0.1134	0.1647	-0.0281	0.0044	0.1647	-0.0215	0.2355	83.1337	23.8367	235.5345
13	1.2054	0.1249	-0.2496	0.8083	0.0266	2.5926	0.0936	-0.1001	0.209	-0.009	0.0306	-0.0851	-0.5768	-0.114	-0.1242	0.2118	0.003	0.0413	0.064	-0.0121	0.2442	83.1705	30.9022	225.0337
14	1.7616	-0.5533	0.0233	1.3036	-0.0136	2.3215	0.1291	-0.0312	0.1917	-0.1356	-0.0325	-0.0957	-0.4991	-0.1213	-0.0966	0.212	0.0181	0.0517	0.1072	-0.0032	0.247	82.6106	29.5019	219.4506
15	5.0936	-1.7085	-1.9654	0.579	0.6587	6.3082	-0.2286	-0.9122	-0.2794	0.0934	0.3187	0.1289	-0.2656	-0.7428	-0.0901	0.1527	0.0773	0.1153	0.4228	0.1327	0.2318	111.88	44.3076	220.0379
16	0.7832	-0.2783	0.1369	1.0224	-0.1165	2.522	0.0499	0.0154	-0.0057	-0.0466	-0.0116	-0.0376	0.2891	-0.3748	-0.0384	0.1573	-0.0386	-0.0118	0.1408	0.0111	0.2849	118.5626	38.2065	198.7864
17	2.9255	-1.9512	0.2741	3.1784	0.2034	5.9444	-0.1648	-0.3233	0.1186	0.1678	0.0829	-0.3129	-0.4435	0.8564	0.0819	0.1104	-0.0781	-0.017	0.1965	0.0267	0.2754	132.6479	52.0929	205.3867
18	1.5356	-0.5615	-0.338	1.3719	0.1562	3.4195	-0.0565	-0.2392	-0.0767	0.0612	0.1085	0.0743	0.3917	-0.4256	-0.0521	0.1978	-0.0575	0.0036	0.1603	0.0496	0.2501	118.122	36.9439	209.0316
19	2.4058	-0.3208	1.2433	0.3056	0.2968	4.8105	-0.0963	-0.7387	-0.2267	0.1604	0.2321	0.0414	0.9703	0.1226	-0.1357	0.3078	0.1537	0.0025	0.3169	0.0725	0.1566	128.5361	29.9728	216.6175
20	3.9034	0.0516	-1.5609	1.5321	0.2742	4.8284	0.2554	-0.5845	0.0934	0.2689	0.1001	-0.0856	0.5663	0.5444	-0.3555	0.2887	0.1063	-0.0551	0.1808	0.0044	0.1781	132.5067	30.4244	212.5183
21	1.9835	-0.9241	-0.3842	1.7272	0.2131	2.7597	0.0195	0.0702	-0.1044	-0.0057	0.0765	-0.0355	0.7182	0.4897	-0.096	0.3783	0.1518	-0.0482	0.1064	-0.0336	0.2042	132.4271	26.7578	198.6803
22	0.4402	-0.1434	0.0851	0.636	0.1596	2.3617	0.0641	0.1586	-0.0171	-0.1257	0.0063	0.0006	0.5603	-0.0077	-0.0704	0.3042	0.0526	-0.0419	0.0886	-0.0325	0.2084	124.0791	31.5349	174.2829
23	9.4146	1.8768	1.1215	2.0911	0.0774	0.1675	0.0679	0.3315	0.6801	-0.7648	-0.2416	-0.6779	0.0281	0.1783	0.1737	0.5321	0.0196	0.2794	0.8001	0.1814	0.4875	143.6752	36.6643	177.0362
24	8.7096	3.9981	4.108	9.9737	0.2499	3.9433	-0.1751	0.3859	-0.0432	-0.4272	-0.0567	-0.2048	-0.4338	1.0147	0.2319	0.4929	0.0287	-0.0703	0.5418	0.0622	0.0817	139.4565	25.4733	165.7521
25	0.8842	-0.2992	0.0982	0.9857	0.2362	2.9901	0.1201	0.1905	0.0346	-0.2369	-0.1027	0.116	0.2162	-0.3771	-0.0174	0.1739	0.0347	-0.0557	0.1745	0.001	0.2131	116.5794	40.5129	170.6033
26	0.2184	0.6221	0.2109	3.298	3.3122	5.9677	-0.1155	0.0257	-0.0239	-0.6062	0.4041	-0.2506	-0.3398	1.1014	-0.2886	0.2076	0.0686	0.1031	0.3394	0.0203	0.1462	134.1943	49.1903	162.9741
27	0.7661	-0.0202	0.1713	1.1508	0.2258	3.193	0.0732	0.1178	0.1554	-0.1894	-0.0467	0.0751	-0.3346	-0.1936	-0.0265	0.1592	0.0612	-0.0102	0.1084	0.0625	0.2589	119.8789	52.0223	175.7712
28	3.2384	1.7416	3.3698	5.043	3.4799	7.4159	-0.2028	-0.0174	0.367	0.0566	0.3181	-0.1971	-0.4591	0.9543	-0.1154	0.1648	-0.0386	0.0013	0.3402	0.0079	0.2971	135.1092	49.1484	184.5299

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 102
2	X-RAY DIFFRACTION	2	A	103 - 144
3	X-RAY DIFFRACTION	3	A	145 - 254
4	X-RAY DIFFRACTION	4	A	255 - 282
5	X-RAY DIFFRACTION	5	A	283 - 292
6	X-RAY DIFFRACTION	6	A	293 - 353
7	X-RAY DIFFRACTION	7	A	354 - 502
8	X-RAY DIFFRACTION	8	B	1 - 83
9	X-RAY DIFFRACTION	9	B	84 - 109
10	X-RAY DIFFRACTION	10	B	110 - 166
11	X-RAY DIFFRACTION	11	B	167 - 217
12	X-RAY DIFFRACTION	12	B	218 - 309
13	X-RAY DIFFRACTION	13	B	310 - 355
14	X-RAY DIFFRACTION	14	B	356 - 501
15	X-RAY DIFFRACTION	15	C	1 - 32
16	X-RAY DIFFRACTION	16	C	33 - 122
17	X-RAY DIFFRACTION	17	C	123 - 163
18	X-RAY DIFFRACTION	18	C	164 - 236
19	X-RAY DIFFRACTION	19	C	237 - 282
20	X-RAY DIFFRACTION	20	C	283 - 334
21	X-RAY DIFFRACTION	21	C	335 - 503
22	X-RAY DIFFRACTION	22	D	1 - 124
23	X-RAY DIFFRACTION	23	D	125 - 163
24	X-RAY DIFFRACTION	24	D	164 - 181
25	X-RAY DIFFRACTION	25	D	182 - 255
26	X-RAY DIFFRACTION	26	D	256 - 304
27	X-RAY DIFFRACTION	27	D	305 - 374
28	X-RAY DIFFRACTION	28	D	375 - 504

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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