PDB-9bnj: Proteus vulgaris tryptophan indole-lyase aminoacrylate complex wi...

ID or keywords:

Entry

Database: PDB / ID: 9bnj

Title

Proteus vulgaris tryptophan indole-lyase aminoacrylate complex with benzimidazole

Components

Tryptophanase

Keywords

LYASE / pyridoxal-5'-phosphate / reaction intermediates / reaction mechanism / aminotransferase fold

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: 1.51 Å

Authors

Phillips, R.S.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Proteus vulgaris tryptophan indole-lyase aminoacrylate complex with benzimidazole
Authors: Phillips, R.S.

History

Deposition	May 2, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bnj.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb9bnj.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	9bnj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bnj_validation.pdf.gz	3.8 MB	Display	wwPDB validaton report
Full document	9bnj_full_validation.pdf.gz	3.8 MB	Display
Data in XML	9bnj_validation.xml.gz	85.3 KB	Display
Data in CIF	9bnj_validation.cif.gz	130.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bn/9bnj ftp://data.pdbj.org/pub/pdb/validation_reports/bn/9bnj	HTTPS FTP

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Related structure data

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: 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)	113.945, 118.225, 152.470
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein , 1 types, 4 molecules ABCD

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28796, tryptophanase

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Non-polymers , 6 types, 1775 molecules

#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-BZI / BENZIMIDAZOLE Mass: 118.136 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₇H₆N₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid Mass: 316.204 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₃N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1760 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.46 Å³/Da / Density % sol: 50.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M potassium phosphate, pH 8.0, 1 mM DTT, 0.1 mM PLP, 0.2 M KCl, 22% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97856 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 3, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.51→91.27 Å / Num. obs: 319496 / % possible obs: 99.41 % / Redundancy: 5.4 % / B_iso Wilson estimate: 20.44 Å² / CC_1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 7.2
Reflection shell	Resolution: 1.51→1.53 Å / Num. unique obs: 20571 / CC_1/2: 0.327 / CC star: 0.558

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
autoPROC		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.51→91.27 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1805	15878	5 %
R_work	0.1577	-	-
obs	0.1588	317636	99.41 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.51→91.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14672	0	138	1768	16578

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	17591
X-RAY DIFFRACTION	f_angle_d	0.789	23830
X-RAY DIFFRACTION	f_dihedral_angle_d	12.826	6780
X-RAY DIFFRACTION	f_chiral_restr	0.05	2553
X-RAY DIFFRACTION	f_plane_restr	0.009	3105

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 (%)
1.51-1.53	0.3229	510	0.3083	9343	X-RAY DIFFRACTION	94
1.53-1.55	0.2947	534	0.297	9678	X-RAY DIFFRACTION	96
1.55-1.57	0.3111	486	0.2945	9845	X-RAY DIFFRACTION	98
1.57-1.59	0.2845	501	0.2728	9893	X-RAY DIFFRACTION	99
1.59-1.61	0.298	501	0.2781	9970	X-RAY DIFFRACTION	99
1.61-1.63	0.32	537	0.2976	9961	X-RAY DIFFRACTION	99
1.63-1.65	0.2834	544	0.2767	9956	X-RAY DIFFRACTION	99
1.65-1.68	0.278	536	0.2605	10069	X-RAY DIFFRACTION	100
1.68-1.7	0.2692	521	0.2424	9955	X-RAY DIFFRACTION	100
1.7-1.73	0.2742	572	0.2311	10017	X-RAY DIFFRACTION	100
1.73-1.76	0.238	492	0.2115	10074	X-RAY DIFFRACTION	100
1.76-1.79	0.2253	501	0.2023	10105	X-RAY DIFFRACTION	100
1.79-1.83	0.2172	528	0.1913	10044	X-RAY DIFFRACTION	100
1.83-1.86	0.2055	534	0.1824	10059	X-RAY DIFFRACTION	100
1.86-1.9	0.2141	522	0.1791	10067	X-RAY DIFFRACTION	100
1.9-1.95	0.1881	513	0.171	10094	X-RAY DIFFRACTION	100
1.95-2	0.2089	527	0.1873	10075	X-RAY DIFFRACTION	100
2-2.05	0.2173	550	0.1866	10084	X-RAY DIFFRACTION	100
2.05-2.11	0.175	541	0.1501	10100	X-RAY DIFFRACTION	100
2.11-2.18	0.1749	544	0.1421	10073	X-RAY DIFFRACTION	100
2.18-2.26	0.1618	551	0.1354	10060	X-RAY DIFFRACTION	100
2.26-2.35	0.1502	485	0.1283	10193	X-RAY DIFFRACTION	100
2.35-2.46	0.1525	520	0.1335	10128	X-RAY DIFFRACTION	100
2.46-2.59	0.1548	538	0.1346	10184	X-RAY DIFFRACTION	100
2.59-2.75	0.1682	540	0.1372	10131	X-RAY DIFFRACTION	100
2.75-2.96	0.1622	525	0.1394	10185	X-RAY DIFFRACTION	100
2.96-3.26	0.1645	582	0.1396	10168	X-RAY DIFFRACTION	100
3.26-3.73	0.1406	542	0.1315	10273	X-RAY DIFFRACTION	100
3.73-4.7	0.1339	487	0.1162	10373	X-RAY DIFFRACTION	100
4.7-91.27	0.1866	614	0.1584	10601	X-RAY DIFFRACTION	100

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	0.9199	-0.1186	0.5006	0.1868	0.0445	0.7572	-0.0516	-0.1244	0.079	0.0443	0.015	-0.0572	-0.0707	-0.024	0.0429	0.1886	-0.0048	-0.005	0.1756	-0.0133	0.1562	59.47	9.432	-1.381
2	1.2011	-0.3404	-0.263	1.3334	0.5617	2.4933	-0.0513	-0.2109	-0.1402	0.0931	0.0439	0.0655	0.1083	-0.191	0.0542	0.154	-0.0216	0.01	0.2017	0.0551	0.1718	39.25	-6.825	10.6
3	4.5141	-0.2523	4.1368	1.8358	0.1594	7.3369	-0.1527	-0.2239	0.0987	0.1087	0.0345	0.0425	-0.3593	0.0594	0.1026	0.2619	0.0127	0.0469	0.3154	0.0119	0.1659	43.882	4.437	22.102
4	1.2342	-0.0921	0.2373	0.1876	-0.0818	1.012	-0.0208	-0.3806	-0.1423	0.08	0.0146	0.0382	0.0806	-0.023	0.0155	0.2113	0.0094	0.0158	0.254	0.0567	0.1638	48.667	-7.655	17.853
5	1.3955	-0.1953	0.8481	0.7058	-0.0255	0.7787	-0.0763	-0.4974	0.0807	0.18	-0.004	-0.0574	-0.0805	-0.2168	0.0081	0.1989	0.0124	0.0111	0.3204	-0.0339	0.1126	59.586	9.131	12.642
6	2.679	-1.7392	-0.6685	1.6226	-0.0306	0.6197	-0.2695	-0.4825	0.68	0.2981	0.0472	0.0306	-0.7761	-1.2367	-0.4141	0.5971	0.3303	0.0026	1.0419	-0.167	0.2423	52.456	25.208	15.963
7	0.7252	-0.0655	0.0388	0.4636	0.033	0.6481	-0.003	-0.019	-0.0221	0.0637	0.0057	0.0849	-0.0169	-0.073	0.0036	0.1787	-0.007	0.0149	0.1263	0	0.1751	30.578	7.473	-13.033
8	1.5262	-0.5704	1.4894	1.5629	-0.5749	1.323	0.1487	-1.1902	-0.6522	0.2342	0.2201	0.5886	0.2845	-1.1053	0.0201	0.3016	-0.1662	0.0307	0.8535	0.2382	0.4584	19.79	-10.501	-15.692
9	0.9772	0.2634	0.3251	0.5111	0.4039	1.1749	0.1056	-0.0935	-0.1991	0.1477	0.0242	-0.1314	0.2616	0.1147	0.0089	0.1787	0.0358	-0.0452	0.1111	-0.0064	0.1851	74.188	-2.998	-15.4
10	3.9993	0.4872	-1.2166	2.2625	0.6265	2.1487	-0.0709	0.3931	-0.0514	-0.1974	0.0888	-0.1504	0.0731	0.2561	0.0224	0.1299	0.0148	0.0199	0.2448	-0.0398	0.1683	89.872	3.559	-37.62
11	0.7508	0.1784	-0.0239	0.3698	0.1559	1.1678	0.02	0.0351	0.0588	-0.015	0.0415	-0.1024	-0.1047	0.3128	-0.0567	0.1487	-0.0211	0.0042	0.1913	-0.02	0.1896	85.883	12.241	-24.911
12	0.2573	-0.243	0.299	0.244	-0.2788	0.3312	0.1471	0.5872	-0.6555	0.0021	0.3562	-0.8809	0.2609	1.0073	0.04	0.2669	0.125	-0.1131	0.7152	-0.3005	0.7226	97.861	-3.131	-9.788
13	0.7694	0.5452	0.3056	1.5261	1.0336	0.8411	0.1433	0.2439	-0.5505	0.1036	0.429	-0.7182	0.3039	0.7629	0.0442	0.2726	0.1776	-0.1179	0.5201	-0.2507	0.5609	91.719	-10.027	-12.441
14	0.6925	0.0508	0.4252	0.6006	0.163	0.9684	-0.0474	0.0415	0.0734	-0.0813	0.0037	0.0129	-0.1463	0.0278	0.0325	0.1957	0.0058	-0.0045	0.1401	-0.0177	0.1844	52.909	2.035	-34.607
15	1.309	0.0476	0.1346	0.9361	0.1704	1.1677	0.0864	0.2856	-0.2982	0.0196	0.0695	-0.1737	0.1794	0.2912	0.0389	0.1878	0.0766	-0.0448	0.2323	-0.1142	0.2829	74.106	-17.763	-37.289
16	2.7202	0.8576	0.2684	2.8137	1.7367	3.126	0.0885	0.726	-0.1348	-0.1953	0.1302	-0.1283	-0.104	0.3049	-0.1748	0.2485	0.0808	0.0023	0.4568	-0.1026	0.2264	69.381	-13.373	-53.083
17	1.2202	0.1228	0.9122	0.2781	0.1725	0.8367	0.1665	0.2954	-0.3215	-0.0151	0.0251	-0.0809	0.2125	0.2082	-0.0241	0.2237	0.0652	-0.0347	0.1744	-0.0957	0.2501	62.301	-19.587	-41.077
18	1.9894	0.2591	-0.7377	1.0533	-1.0357	1.2932	-0.1999	1.1004	-0.1995	-0.5331	0.3868	-0.0999	-0.2915	0.3382	-0.061	0.4163	-0.1098	0.0063	0.4684	-0.0532	0.1824	50.466	-4.503	-57.398
19	1.9128	0.9054	0.1043	1.3754	-0.4295	1.7231	-0.2266	0.497	-0.1051	-0.3467	0.1238	-0.1042	-0.0746	0.1421	0.1198	0.2202	-0.0238	0.0147	0.2139	-0.0442	0.1574	53.072	0.023	-51.191
20	6.9603	1.5798	-2.0865	3.6071	-0.8055	3.6594	-0.1388	0.6932	0.5823	-0.5191	0.209	-0.1334	-0.2994	0.2466	-0.048	0.5271	-0.1168	0.0581	0.3997	-0.0073	0.2209	59.042	8.687	-57.158

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN C AND RESID 2:75 )	C	2 - 75
2	X-RAY DIFFRACTION	2	( CHAIN C AND RESID 76:132 )	C	76 - 132
3	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 133:155 )	C	133 - 155
4	X-RAY DIFFRACTION	4	( CHAIN C AND RESID 156:295 )	C	156 - 295
5	X-RAY DIFFRACTION	5	( CHAIN C AND RESID 296:437 )	C	296 - 437
6	X-RAY DIFFRACTION	6	( CHAIN C AND RESID 438:466 )	C	438 - 466
7	X-RAY DIFFRACTION	7	( CHAIN D AND RESID 2:341 )	D	2 - 341
8	X-RAY DIFFRACTION	8	( CHAIN D AND RESID 342:466 )	D	342 - 466
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 2:99 )	A	2 - 99
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 100:141 )	A	100 - 141
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 142:341 )	A	142 - 341
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 342:371 )	A	342 - 371
13	X-RAY DIFFRACTION	13	( CHAIN A AND RESID 372:466 )	A	372 - 466
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 2:75 )	B	2 - 75
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 76:132 )	B	76 - 132
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 133:155 )	B	133 - 155
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 156:342 )	B	156 - 342
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 343:371 )	B	343 - 371
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 372:437 )	B	372 - 437
20	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 438:466 )	B	438 - 466

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