PDB-9blv: Proteus vulgaris tryptophan indole-lyase complexed with L-Trp and...

ID or keywords:

Entry

Database: PDB / ID: 9blv

Title

Proteus vulgaris tryptophan indole-lyase complexed with L-Trp and 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: 1.78 Å

Authors

Phillips, R.S.

Funding support

United States, 1items

Citation

Journal: Acs Catalysis / Year: 2024
Title: Structural Snapshots of Proteus vulgaris Tryptophan Indole-Lyase Reveal Insights into the Catalytic Mechanism.
Authors: Phillips, R.S. / Brown, S.M. / Patel, R.S.

History

Deposition	May 1, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9blv.cif.gz	755.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9blv.ent.gz		Display	PDB format
PDBx/mmJSON format	9blv.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/bl/9blv ftp://data.pdbj.org/pub/pdb/validation_reports/bl/9blv	HTTPS FTP

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Related structure data

Related structure data	8v6pC 8v9pC 9bnjC C: citing same article (ref.)
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
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

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)	113.523, 109.962, 144.982
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 , 7 types, 946 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.: 2 / Source method: obtained synthetically / Formula: C₇H₆N₂
#4: 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.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₃N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#6: Chemical	ChemComp-PLT / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-L-TRYPTOPHANE Mass: 433.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₂₀N₃O₇P
#7: Chemical	ChemComp-A1A2Z / N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tryptophan Mass: 435.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₁₉H₂₂N₃O₇P / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 934 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	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: 2.18 Å³/Da / Density % sol: 43.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M potassium phosphate, pH 8, 0.2 M CsCl, 22% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.776→56.76 Å / Num. obs: 94968 / % possible obs: 94.4 % / Redundancy: 5.8 % / B_iso Wilson estimate: 19.86 Å² / CC_1/2: 0.994 / CC star: 0.998 / Net I/σ(I): 5.4
Reflection shell	Resolution: 1.776→1.8 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4748 / CC_1/2: 0.666

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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: 1.78→56.76 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2474	4846	5.11 %
R_work	0.1978	-	-
obs	0.2003	94874	54.33 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.78→56.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14564	0	132	936	15632

Refine LS restraints

Type: f_plane_restr / Dev ideal: 0.007 / Number: 2678

LS refinement shell

Resolution: 1.776→1.8 Å /

	R_factor	Num. reflection
R_free	0.6909	3
R_work	0.3153	48

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	1.1463	0.0696	-0.0869	0.3456	0.1176	0.9547	-0.0335	0.1291	0.1288	-0.0323	0.0608	0.1144	0.0127	-0.3146	-0.0052	0.0951	-0.0254	0.0029	0.2097	0.0851	0.1284	-26.2697	-9.796	50.9901
2	0.7808	-0.1167	-0.119	0.8963	0.0028	0.1703	-0.1207	0.1651	0.2785	-0.0231	0.2484	0.2257	0.0386	-0.3697	-0.0013	0.0804	0.0354	0.0291	0.4292	0.1	0.2744	-34.7426	5.0389	62.7588
3	1.1	-0.3962	0.8676	0.4845	-0.2081	0.7912	-0.2025	0.1929	0.6853	0.024	0.181	0.1424	-0.2431	-0.3913	-0.0448	0.2487	0.0981	0.0129	0.7549	0.3339	0.6412	-37.8895	15.0362	53.7085
4	0.7836	0.1502	-0.303	0.5677	-0.4278	1.6123	-0.0652	0.0746	0.1148	-0.0984	0.0496	0.0373	0.0938	-0.009	0.0517	0.1185	-0.0081	-0.0219	0.1015	0.0924	0.1097	-1.742	-0.5685	39.0868
5	1.0996	0.0227	1.0478	0.9572	-0.0055	2.8024	-0.0544	0.1942	0.1793	-0.1738	0.1343	0.2472	-0.2161	-0.1877	0.1948	0.2038	-0.0013	-0.0568	0.5766	0.2173	0.2727	-21.9724	6.8972	23.5924
6	0.1671	0.1441	-0.15	0.1634	-0.1042	0.2956	-0.0408	0.4574	0.3338	-0.1714	0.2263	0.2237	-0.2242	-0.3623	0.2787	0.2114	0.0148	-0.0705	0.3582	0.3816	0.1549	-7.5294	12.3277	26.4126
7	0.6732	-0.0294	-0.6267	0.7604	-0.8571	1.6091	-0.249	0.5071	-0.1055	-0.5134	0.3148	0.1678	0.4999	-0.5163	0.4151	0.3246	-0.1828	0.0327	0.4558	0.059	0.0499	2.3531	-9.129	17.5886
8	0.7058	0.257	0.7198	0.665	0.2022	1.1468	-0.0289	0.4566	-0.0793	-0.3234	0.0115	0.2606	0.4878	-0.4557	-0.3431	0.3222	-0.1356	-0.0918	0.6355	0.06	0.1144	-1.0753	-11.9004	20.2398
9	1.1754	-0.0531	-0.0189	0.2668	0.1827	0.9927	-0.2668	-0.3127	-0.0629	0.1063	0.0465	0.0534	0.0979	-0.1918	0.0991	0.1541	0.0809	0.0282	0.2471	0.0387	0.1712	1.7241	-0.3848	71.5407
10	0.2611	-0.5205	0.5559	1.4321	-0.0886	3.8639	-0.0893	-0.3432	0.1765	0.239	0.1354	-0.1701	-0.1358	0.2954	-0.0642	0.2026	0.0847	-0.0294	0.2283	-0.1049	0.1286	21.9861	7.1726	87.2989
11	0.3207	-0.2137	-0.0483	0.1554	0.0592	0.2758	-0.1028	-0.415	0.3086	0.1469	0.0723	0.0987	-0.1542	-0.3579	-0.0363	0.1316	0.1148	-0.0151	0.4269	-0.1603	0.1279	6.3983	11.5802	85.1458
12	0.3868	0.4676	-0.4233	0.8681	-0.3184	0.5985	-0.1359	-0.6176	-0.049	0.5038	0.1829	-0.0264	0.2888	0.5843	0.0443	0.4822	0.254	0.1059	1.0114	0.0874	0.2856	0.9242	-12.8695	94.6269
13	1.7197	-0.0686	-0.6087	0.5768	0.3729	0.426	-0.1946	-0.531	-0.3674	0.2049	0.072	0.0416	0.1586	0.1064	0.3326	0.1734	0.0986	0.065	0.5769	0.0339	0.197	-9.512	-5.5402	83.4641
14	1.8656	-0.2641	-1.2252	1.1251	1.3947	2.1785	0.04	-0.6724	-0.8536	0.8255	0.063	0.3114	0.4185	0.0463	0.036	0.6237	0.0323	0.0791	0.712	0.2932	0.548	5.3026	-19.7232	92.2242
15	1.0203	0.0367	-0.4038	0.3187	0.0407	1.325	0.1854	0.0605	0.3817	-0.0633	0.1087	-0.038	-0.3434	0.3692	-0.1413	0.2039	-0.0857	0.0221	0.3462	-0.0129	0.1653	16.6003	4.8919	51.0833
16	2.4554	0.3067	-0.11	0.9106	0.2072	0.6978	0.1026	-0.066	0.022	0.0353	-0.0496	-0.0073	0.052	0.0679	-0.0695	0.1302	0.0011	-0.0511	0.0674	-0.006	0.0759	26.7487	-11.8983	71.0069
17	0.765	-0.1667	0.2964	0.5209	0.0748	0.7079	0.0849	0.349	-0.1498	0.0019	0.0213	-0.0442	0.088	0.0904	-0.0466	0.0577	0.024	-0.0627	0.1698	-0.087	0.1062	30.2687	-14.7302	61.8478
18	0.6722	-0.1841	-0.6877	0.1847	-0.0882	1.2784	0.0541	-0.0452	0.1601	-0.0345	0.0598	-0.1764	-0.2542	0.5777	-0.2268	0.1543	-0.073	0.0566	0.6831	-0.0285	0.1099	33.1255	-1.5818	42.9259
19	1.4574	0.1227	0.4958	1.1112	0.7618	0.635	0.0952	-0.2379	0.497	0.1046	0.285	-0.4383	-0.3639	0.7553	0.6726	0.2501	-0.2214	0.0181	0.8547	-0.1563	0.3402	34.1787	11.1129	50.9916

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 341 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 342 through 437 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 438 through 466 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 99 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 100 through 141 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 142 through 341 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 342 through 396 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 397 through 466 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 2 through 99 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 100 through 141 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 142 through 358 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 359 through 411 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 412 through 438 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 439 through 466 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 2 through 75 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 76 through 141 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 142 through 321 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 322 through 367 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 368 through 465 )

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