PDB-5ixj: Tryptophan Synthase beta-subunit from Pyrococcus furiosus with L-...

ID or keywords:

Entry

Database: PDB / ID: 5ixj

Title

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

Components

Tryptophan synthase beta chain 1

Keywords

LYASE / Substrate analog / PLP / Fold-type II

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 /

MOLECULAR REPLACEMENT / Resolution: 1.54 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2016
Title: Synthesis of beta-Branched Tryptophan Analogues Using an Engineered Subunit of Tryptophan Synthase.
Authors: Herger, M. / van Roye, P. / Romney, D.K. / Brinkmann-Chen, S. / Buller, A.R. / Arnold, F.H.

History

Deposition	Mar 23, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 17, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ixj.cif.gz	613.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5ixj.ent.gz	505.5 KB	Display	PDB format
PDBx/mmJSON format	5ixj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ixj_validation.pdf.gz	480.6 KB	Display	wwPDB validaton report
Full document	5ixj_full_validation.pdf.gz	487.1 KB	Display
Data in XML	5ixj_validation.xml.gz	62.5 KB	Display
Data in CIF	5ixj_validation.cif.gz	89.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ix/5ixj ftp://data.pdbj.org/pub/pdb/validation_reports/ix/5ixj	HTTPS FTP

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Related structure data

Related structure data	5dw3S S: Starting model for refinement
Similar structure data	6am7-2 2dh5-1 3l7r-d 6amc-2 6amc-1 1x1q-d 1v8z-2 1v8z-1 3tte-1 6amh-1 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

D: Tryptophan synthase beta chain 1

hetero molecules

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

2

B: Tryptophan synthase beta chain 1

C: Tryptophan synthase beta chain 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.718, 112.367, 160.310
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) / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical	ChemComp-THR / THREONINE Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₉NO₃
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 842 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.03 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 15-25% PEG3350, 0.1 M HEPES pH 7.5 / PH range: 7.5-8.0

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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: 1.54→40 Å / Num. obs: 214599 / % possible obs: 98.9 % / Redundancy: 9.8 % / CC_1/2: 1 / R_merge(I) obs: 0.064 / Net I/σ(I): 19.4
Reflection shell	Resolution: 1.54→1.57 Å / Redundancy: 5.5 % / R_merge(I) obs: 1.403 / Mean I/σ(I) obs: 1.3 / % possible all: 78.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
XDS		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5DW3

5dw3

Resolution: 1.54→40 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.964 / SU B: 3.405 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.075 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19486	11224	5 %	RANDOM
R_work	0.17508	-	-	-
obs	0.17607	214599	97.66 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 25.067 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.54 Å²	0 Å²	0 Å²
2-	-	0.38 Å²	-0 Å²
3-	-	-	-0.92 Å²

Refinement step

Cycle: LAST / Resolution: 1.54→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11797	0	36	842	12675

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	12359
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11913
X-RAY DIFFRACTION	r_angle_refined_deg	1.176	1.968	16781
X-RAY DIFFRACTION	r_angle_other_deg	0.705	3	27346
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.175	5	1615
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.655	23.73	512
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.89	15	2033
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.731	15	69
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1856
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	14156
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2817
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	0.695	1.103	6314
X-RAY DIFFRACTION	r_mcbond_other	0.695	1.103	6313
X-RAY DIFFRACTION	r_mcangle_it	1.139	1.648	7908
X-RAY DIFFRACTION	r_mcangle_other	1.139	1.649	7909
X-RAY DIFFRACTION	r_scbond_it	1.15	1.244	6045
X-RAY DIFFRACTION	r_scbond_other	1.15	1.244	6045
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.84	1.811	8850
X-RAY DIFFRACTION	r_long_range_B_refined	5.497	9.967	14589
X-RAY DIFFRACTION	r_long_range_B_other	5.451	9.377	14187
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.539→1.579 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	694	-
R_work	0.307	13558	-
obs	-	-	84.24 %

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	0.2648	0.1072	-0.0945	0.3724	0.1967	0.9826	0.0277	0.011	0.0415	0.0074	0.0032	-0.0135	-0.034	0.0205	-0.0309	0.0938	-0.0075	0.0064	0.1449	0.006	0.1008	7.869	-13.957	33.702
2	2.1189	-0.6895	-0.3438	2.0909	0.8539	2.0042	0.1972	0.1439	0.0223	-0.1647	-0.2345	0.1782	-0.3275	-0.5055	0.0373	0.1539	0.1264	0.0064	0.2492	0.0094	0.0677	-7.282	-1.071	32.407
3	0.2488	0.1078	-0.3534	0.2937	-0.1064	1.2026	-0.007	0.1022	-0.011	-0.0343	0.0298	-0.0634	0.0528	-0.1061	-0.0228	0.112	-0.0104	-0.0016	0.1675	0.003	0.0918	2.537	-21.264	26.269
4	0.197	0.061	0.6614	2.3237	-4.8278	13.8046	0.0059	0.0461	0.0194	0.0327	0.1802	0.0158	-0.3043	-0.4789	-0.1862	0.1789	0.0764	0.0406	0.3581	0.0661	0.1717	-13.222	-13.948	22.054
5	0.4883	-0.0184	-0.4676	0.5051	-0.2314	2.1766	0.0021	0.124	-0.0597	-0.0372	0.018	0.0428	0.1873	-0.3693	-0.0201	0.1074	-0.065	-0.0123	0.199	-0.0041	0.0691	-6.946	-27.347	31.536
6	0.7035	-0.5939	-0.5284	1.6969	-0.2816	1.0207	-0.0362	0.0153	-0.0196	-0.0379	0.0755	0.0598	0.1504	-0.271	-0.0393	0.138	-0.0686	-0.0162	0.2544	0.0113	0.0807	-6.623	-27.863	39.313
7	0.2459	-0.0212	0.1221	0.5925	-0.071	0.8846	-0.0365	-0.0063	0.0223	0.0031	-0.0023	0.0136	-0.1304	-0.0088	0.0388	0.1078	0.0148	-0.0066	0.1448	-0.0042	0.0921	36.061	-36.42	47.055
8	2.305	0.4214	-1.5598	1.8142	-1.5285	4.4052	0.0927	-0.2963	-0.1039	0.1408	-0.431	-0.2092	-0.5589	1.0426	0.3383	0.1387	-0.1812	-0.0674	0.3281	0.0852	0.0748	53.2	-28.948	48.626
9	0.1577	-0.0197	0.329	0.5126	0.1796	1.2213	-0.031	-0.0556	-0.0133	0.089	0.0205	0.0596	0.0344	0.0153	0.0105	0.1069	0.012	0.0081	0.1747	0.0042	0.0844	38.423	-47.508	53.636
10	1.4886	-0.5684	1.6056	2.8106	2.6128	5.8846	-0.0363	0.0033	0.2043	-0.0601	0.2656	-0.376	-0.1746	0.5936	-0.2293	0.0833	-0.0766	0.0113	0.5739	-0.1104	0.1453	55.502	-45.5	54.965
11	0.7132	-0.0932	-0.0511	0.5071	0.1017	1.412	0.0112	-0.0045	-0.0888	0.0184	-0.0124	0.0073	0.1716	0.1871	0.0012	0.1139	0.0418	-0.0025	0.1533	0.0113	0.0814	42.626	-55.701	45.271
12	15.7635	-9.207	-2.5403	5.3908	1.4795	0.411	-0.1424	-0.4214	0.1553	0.0664	0.1747	-0.1078	0.0275	0.0949	-0.0323	0.0737	0.1362	-0.0176	0.4846	-0.0361	0.114	61.193	-52.754	36.148
13	0.3231	0.0231	-0.0292	0.3642	-0.2243	0.6494	-0.0602	0.0782	0.0132	-0.0146	0.0301	-0.0158	0.0896	-0.0463	0.03	0.1101	-0.0178	-0	0.1682	-0.001	0.0829	33.813	-46.576	16.528
14	2.3001	0.3743	-0.5217	0.7951	-0.6163	2.4369	-0.105	0.1261	0.0844	-0.0417	-0.0624	-0.0161	0.1749	0.2851	0.1675	0.103	0.0423	0.0149	0.1927	0.0219	0.0681	51.792	-52.403	16.472
15	0.3296	-0.0292	0.0165	0.5894	0.2265	0.7745	-0.0726	0.1602	0.0224	-0.0825	0.0274	0.0821	-0.0176	-0.0713	0.0451	0.1275	-0.0076	-0.0097	0.2017	0.0115	0.0727	32.05	-40.542	12.828
16	0.911	0.2744	-0.3066	1.0365	1.1895	3.1054	0.0264	0.0634	0.0619	-0.2074	-0.0051	-0.023	-0.2401	0.3321	-0.0213	0.1325	-0.0446	0.0096	0.2695	0.042	0.0335	48.418	-35.164	0.463
17	0.8247	0.1099	0.3104	0.4106	0.5677	2.2194	-0.0049	0.1178	0.1232	-0.0716	0.0296	-0.0329	-0.2079	0.2194	-0.0247	0.1318	-0.0414	-0.0019	0.1626	0.0483	0.0665	42.811	-30.683	14.092
18	1.0422	-0.5327	0.3458	0.9304	0.2449	1.0033	-0.0386	0.0421	0.0829	-0.0507	0.0005	-0.0183	-0.2297	0.1779	0.0381	0.1525	-0.0402	-0.0125	0.1753	0.0361	0.0912	40.4	-27.788	22.645
19	0.2957	0.0812	-0.0739	0.1499	-0.0278	0.6335	-0.0099	-0.0547	0.0063	0.0634	0.0424	-0.0144	0.1115	-0.0018	-0.0325	0.1617	-0.0006	-0.0001	0.149	0.0113	0.0731	-0.25	-23.979	63.603
20	1.1881	-0.5195	-0.0144	2.4235	0.4072	5.879	-0.0665	0.0675	0.0366	0.199	0.1704	0.25	-0.4275	-0.5598	-0.1039	0.1433	0.0468	0.0542	0.2042	0.0504	0.068	-17.76	-20.063	62.56
21	0.4106	0.1036	-0.1946	0.3138	-0.1888	0.9006	-0.0066	-0.1425	0.0228	0.1165	0.0407	-0.0346	0.0776	0.0334	-0.0341	0.1488	0.0091	-0.0017	0.2019	-0.0095	0.0553	2.974	-16.236	70.434
22	2.3836	1.8615	-2.3631	3.866	-3.3899	9.5073	0.0446	-0.1126	0.2011	0.2755	0.3266	0.7867	-0.0466	-0.7965	-0.3712	0.1549	0.0595	0.1097	0.4813	0.1195	0.2223	-10.504	-7.13	71.714
23	0.622	-0.0071	0.0139	0.4526	-0.2342	1.2191	0.0262	-0.0855	0.1398	0.0422	0.038	0.0083	-0.1235	-0.0315	-0.0642	0.1165	0.0074	0.0103	0.1476	-0.038	0.0925	4.56	-4.374	62.092
24	1.2936	-1.3621	-0.3167	2.7525	0.6341	0.1916	0.214	0.1612	0.426	-0.0808	-0.1289	-0.7172	-0.0458	-0.0484	-0.0851	0.1162	0.0282	0.0055	0.2387	0.0084	0.2963	-16.616	9.279	52.124

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 128
2	X-RAY DIFFRACTION	2	A	129 - 172
3	X-RAY DIFFRACTION	3	A	173 - 282
4	X-RAY DIFFRACTION	4	A	283 - 300
5	X-RAY DIFFRACTION	5	A	301 - 356
6	X-RAY DIFFRACTION	6	A	357 - 384
7	X-RAY DIFFRACTION	6	A	401
8	X-RAY DIFFRACTION	7	B	1 - 126
9	X-RAY DIFFRACTION	8	B	127 - 180
10	X-RAY DIFFRACTION	9	B	181 - 282
11	X-RAY DIFFRACTION	10	B	283 - 301
12	X-RAY DIFFRACTION	11	B	302 - 378
13	X-RAY DIFFRACTION	12	B	379 - 391
14	X-RAY DIFFRACTION	12	B	401
15	X-RAY DIFFRACTION	13	C	1 - 109
16	X-RAY DIFFRACTION	14	C	110 - 170
17	X-RAY DIFFRACTION	15	C	171 - 254
18	X-RAY DIFFRACTION	16	C	255 - 288
19	X-RAY DIFFRACTION	17	C	289 - 353
20	X-RAY DIFFRACTION	18	C	354 - 384
21	X-RAY DIFFRACTION	18	C	401
22	X-RAY DIFFRACTION	19	D	1 - 136
23	X-RAY DIFFRACTION	20	D	137 - 169
24	X-RAY DIFFRACTION	21	D	170 - 282
25	X-RAY DIFFRACTION	22	D	283 - 301
26	X-RAY DIFFRACTION	23	D	302 - 383
27	X-RAY DIFFRACTION	24	D	384 - 396
28	X-RAY DIFFRACTION	24	D	401

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Yorodumi