PDB-5w19: Tryptophan indole-lyase complex with oxindolyl-L-alanine

ID or keywords:

Entry

Database: PDB / ID: 5w19

Title

Tryptophan indole-lyase complex with oxindolyl-L-alanine

Components

Tryptophanase

Keywords

LYASE / pyridoxal-5'-phosphate / aminotransferase fold / tryptophan metabolism / inhibition

Function / homology

Function and homology information

tryptophanase activity / tryptophanase
Similarity search - Function

Biological species

Proteus vulgaris (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Phillips, R.S. / Wood, Z.A.

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The crystal structure of Proteus vulgaris tryptophan indole-lyase complexed with oxindolyl-L-alanine: implications for the reaction mechanism.
Authors: Phillips, R.S. / Buisman, A.A. / Choi, S. / Hussaini, A. / Wood, Z.A.

History

Deposition	Jun 2, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 6, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 19, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 4, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5w19.cif.gz	905.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5w19.ent.gz	644.8 KB	Display	PDB format
PDBx/mmJSON format	5w19.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5w19_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	5w19_full_validation.pdf.gz	1.9 MB	Display
Data in XML	5w19_validation.xml.gz	71.1 KB	Display
Data in CIF	5w19_validation.cif.gz	96.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w1/5w19 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/5w19	HTTPS FTP

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Related structure data

Related structure data	5w1bC 1ax4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2c44-d 2ycp-d 2vlh-1 2ycn-1 2yct-1 2ez2-1 6dyt-1 6mqq-1 1ax4-d 2vlf-1 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

Deposited unit

A: Tryptophanase

B: Tryptophanase

C: Tryptophanase

D: Tryptophanase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	62.117, 152.081, 211.363
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(z,x,y)

#1: Protein	Tryptophanase / L-tryptophan indole-lyase / TNase Mass: 52558.984 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: tnaA / Plasmid: pET100b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28796, tryptophanase
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-9TD / 1-carboxy-1-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]azaniumyl}-2-[(3R)-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-ide Mass: 449.351 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₉H₂₀N₃O₈P
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.37 Å³/Da / Density % sol: 48.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 35 mM potassium phosphate, 0.05 M HEPES, 0.3 M KCl, 11% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.099→48.092 Å / Num. obs: 117489 / % possible obs: 98.75 % / Redundancy: 14.8 % / B_iso Wilson estimate: 48.17 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.2139 / R_pim(I) all: 0.05764 / R_rim(I) all: 0.2216 / Net I/σ(I): 9.84
Reflection shell	Resolution: 2.099→2.174 Å / Redundancy: 14.9 % / R_merge(I) obs: 6.921 / Mean I/σ(I) obs: 0.43 / Num. unique obs: 11609 / CC_1/2: 0.272 / R_pim(I) all: 1.851 / % possible all: 88.98

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1AX4

1ax4

Resolution: 2.1→48.106 Å / SU ML: 0.432 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 35.21
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.244	11077	5.04 %
R_work	0.2168	208592	-
obs	0.218	219669	97.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 74.82 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→48.106 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14752	0	128	537	15417

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	15356
X-RAY DIFFRACTION	f_angle_d	0.495	20782
X-RAY DIFFRACTION	f_chiral_restr	0.0425	2227
X-RAY DIFFRACTION	f_plane_restr	0.0035	2713
X-RAY DIFFRACTION	f_dihedral_angle_d	13.37	9262

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 (%)
2.1009-2.1248	0.4427	216	0.4724	3840	X-RAY DIFFRACTION	53.98
2.12-2.14	0.4407	345	0.4357	6306	X-RAY DIFFRACTION	87.84
2.14-2.17	0.4274	361	0.4311	6552	X-RAY DIFFRACTION	92.6
2.17-2.2	0.4251	362	0.4131	6990	X-RAY DIFFRACTION	96.74
2.2-2.23	0.4343	373	0.4282	6919	X-RAY DIFFRACTION	97.51
2.23-2.26	0.4066	386	0.4109	6977	X-RAY DIFFRACTION	98.77
2.26-2.29	0.4512	396	0.4048	7108	X-RAY DIFFRACTION	99.14
2.29-2.32	0.4237	394	0.386	7056	X-RAY DIFFRACTION	99.46
2.32-2.36	0.3861	342	0.383	7164	X-RAY DIFFRACTION	99.61
2.36-2.4	0.3804	388	0.375	7140	X-RAY DIFFRACTION	99.7
2.4-2.44	0.3851	362	0.3569	7057	X-RAY DIFFRACTION	99.67
2.44-2.49	0.3393	394	0.3453	7180	X-RAY DIFFRACTION	99.94
2.49-2.53	0.3564	375	0.327	7068	X-RAY DIFFRACTION	99.73
2.53-2.59	0.3398	381	0.3265	7186	X-RAY DIFFRACTION	99.73
2.59-2.6	0.3235	367	0.3044	7082	X-RAY DIFFRACTION	99.75
2.64-2.7	0.2926	402	0.2855	7105	X-RAY DIFFRACTION	99.76
2.7-2.77	0.3167	339	0.2768	7117	X-RAY DIFFRACTION	99.89
2.77-2.85	0.3043	386	0.2683	7172	X-RAY DIFFRACTION	99.94
2.85-2.93	0.2818	379	0.2489	7162	X-RAY DIFFRACTION	99.77
2.93-3.02	0.2888	365	0.2445	7082	X-RAY DIFFRACTION	99.89
3.02-3.13	0.2964	365	0.2397	7181	X-RAY DIFFRACTION	99.9
3.13-3.26	0.2491	339	0.2206	7203	X-RAY DIFFRACTION	99.8
3.26-3.41	0.2682	349	0.2095	7061	X-RAY DIFFRACTION	99.82
3.41-3.59	0.2468	392	0.2051	7129	X-RAY DIFFRACTION	99.9
3.59-3.81	0.2132	349	0.1773	7169	X-RAY DIFFRACTION	99.85
3.81-4.11	0.1987	388	0.1676	7150	X-RAY DIFFRACTION	99.88
4.11-4.52	0.175	408	0.1434	7070	X-RAY DIFFRACTION	99.89
4.52-5.17	0.1617	380	0.1355	7145	X-RAY DIFFRACTION	99.97
5.17-6.52	0.2034	385	0.1668	7116	X-RAY DIFFRACTION	99.98
6.52-48.11	0.1702	409	0.1469	7105	X-RAY DIFFRACTION	99.82

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	0.824	-0.254	-0.402	2.157	0.009	1.755	0.002	-0.155	0.082	0.341	-0.065	0.084	-0.129	-0.095	0.041	0.866	-0.026	0.033	0.411	0.011	0.362	74.805	199.669	46.927
2	1.01	-0.116	0.019	1.666	0.606	1.696	-0.003	-0.336	-0.025	0.59	-0.017	0.352	0.031	-0.246	0.018	0.993	-0.04	0.172	0.596	0.028	0.45	65.646	196.052	55.835
3	1.962	0.513	-0.389	3.047	0.44	2.374	0.224	-0.708	0.193	1.575	-0.257	-0.28	-0.157	0.303	-0.036	1.644	-0.083	-0.018	0.707	0.047	0.495	86.041	193.465	62.829
4	1.758	-0.086	-0.018	2.079	0.018	0.646	-0.048	-0.016	0.123	-0.196	0.091	0.323	-0.314	-0.265	-0.051	1.001	0.025	-0.032	0.419	0.019	0.444	74.104	212.168	24.526
5	1.701	-1.297	-0.314	2.941	1.612	3.156	0.0517	-0.118	0.127	0.181	0.1	-0.08	-0.536	0.113	-0.177	1.019	-0.069	0.002	0.405	0.004	0.366	87.897	220.714	47.913
6	0.715	0.172	-0.044	1.713	0.333	1.74	0.031	-0.157	0.178	0.101	0.101	-0.054	-0.705	0.021	-0.129	1.295	-0.084	-0.016	0.455	-0.04	0.467	89.306	229.296	39.868
7	1.493	-1.25	0.204	3.813	-1.068	1.904	0.188	0.09	0.19	-0.608	-0.1125	0.28	-0.455	-0.157	-0.042	1.263	-0.022	-0.014	0.383	-0.044	0.459	80.823	224.283	26.524
8	3.868	-1.055	-2.145	2.983	0.637	3.78	0.252	-0.107	0.423	0.102	0.06	0.639	-0.745	-0.577	-0.367	1.459	0.092	0.008	0.571	0.043	0.687	66.564	229.128	27.514
9	0.821	-0.385	-0.169	1.889	0.134	1.475	0.03	0.102	-0.118	-0.247	0.082	-0.061	0.389	0.097	-0.099	0.925	-0.0529	-0.057	0.377	-0.032	0.393	95.404	172.343	20.48
10	2.15	-0.607	1.65	2.425	0.055	1.964	0.551	0.334	-0.723	-1.115	0.038	0.653	1.443	-0.034	-0.248	1.763	-0.06	-0.253	0.484	-0.003	0.772	78.935	158.947	24.18
11	0.949	0.265	-0.017	1.243	-0.791	2.22	0.025	0.11	-0.065	-0.29	-0.161	-0.219	-0.291	0.322	0.093	0.992	-0.098	-0.002	0.454	0.032	0.407	89.087	201.572	11.036
12	3.508	-0.473	-2.553	1.17	1.393	5.687	0.092	0.216	-0.299	-0.79	-0.166	0.166	0.169	-0.107	0.137	1.263	-0.061	-0.194	0.425	0.002	0.533	75.433	179.604	-1.146
13	4.247	-4.096	2.317	6.198	-3.433	4.026	-0.19	0.045	0.449	-0.133	-0.104	-0.662	-0.084	0.15	0.23	1.702	-0.101	0.002	0.669	-0.065	0.574	84.56	186.94	-12.89
14	1.01	-0.297	-0.367	0.377	-0.084	1.466	0.126	0.268	-0.182	-0.855	-0.101	0.27	0.371	-0.299	0.024	1.429	-0.09	-0.205	0.585	-0.026	0.4963	72.115	189.344	-7.273
15	1.605	0.245	-0.356	2.24	-1.443	2.481	0.134	0.231	0.099	-0.515	-0.055	-0.088	-0.354	0.032	-0.087	1.295	-0.019	-0.035	0.489	-0.023	0.371	81.864	201.546	-0.631
16	3.064	-1.466	-0.273	2.076	-0.027	2.419	0.193	0.628	0.065	-0.893	-0.284	-0.603	0.094	0.671	0.144	1.741	0.004	0.151	0.785	0.071	0.536	96.459	201.653	-6.023

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 132 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 133 through 371 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 372 through 467 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 75 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 76 through 132 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 133 through 295 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 296 through 371 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 372 through 467 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 2 through 342 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 343 through 467 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 2 through 75 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 76 through 132 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 133 through 155 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 156 through 295 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 296 through 371 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 372 through 467 )

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