PDB-8v2k: Proteus vulgaris tryptophan indole-lyase complexed with L-alanine

ID or keywords:

Entry

Database: PDB / ID: 8v2k

Title

Proteus vulgaris tryptophan indole-lyase complexed with L-alanine

Components

Tryptophanase

Keywords

LYASE / pyridoxal-5'-phosphate / fold I / tetramer

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: 1.81 Å

Authors

Phillips, R.S.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Proteus vulgaris tryptophan indole-lyase complexed with L-alanine
Authors: Phillips, R.S.

History

Deposition	Nov 22, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8v2k.cif.gz	891.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8v2k.ent.gz	608.7 KB	Display	PDB format
PDBx/mmJSON format	8v2k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8v2k_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8v2k_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8v2k_validation.xml.gz	75.6 KB	Display
Data in CIF	8v2k_validation.cif.gz	107.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v2/8v2k ftp://data.pdbj.org/pub/pdb/validation_reports/v2/8v2k	HTTPS FTP

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Related structure data

Related structure data	8v6pC 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

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)	66.889, 113.073, 120.332
Angle α, β, γ (deg.)	90.000, 98.330, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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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 , 5 types, 1088 molecules

#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-F0G / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine / PLP-Ala Type: L-peptide linking / Mass: 318.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-PLI / (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOIC ACID Mass: 318.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1078 / 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: 2.15 Å³/Da / Density % sol: 42.67 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion Details: 0.1 M potassium phosphate, pH 8.0, 0.1 mM pyrodoxal-5'-phosphate, 1 mM DTT, 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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979493 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979493 Å / Relative weight: 1
Reflection	Resolution: 1.81→119.06 Å / Num. obs: 114075 / % possible obs: 93.6 % / Redundancy: 3.5 % / B_iso Wilson estimate: 22.05 Å² / CC_1/2: 0.991 / Net I/σ(I): 5
Reflection shell	Resolution: 1.81→1.875 Å / Num. unique obs: 5704 / CC_1/2: 0.669

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
autoPROC	1.20.1_4487	data processing
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.81→119.06 Å / SU ML: 0.2213 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2312	5711	5.01 %
R_work	0.1863	108348	-
obs	0.1885	114059	70.48 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.71 Å²

Refinement step

Cycle: LAST / Resolution: 1.81→119.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14614	0	96	1079	15789

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0032	15153
X-RAY DIFFRACTION	f_angle_d	0.5863	20489
X-RAY DIFFRACTION	f_chiral_restr	0.0457	2206
X-RAY DIFFRACTION	f_plane_restr	0.0062	2667
X-RAY DIFFRACTION	f_dihedral_angle_d	12.1781	5691

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 (%)
1.81-1.83	0.3605	9	0.2638	155	X-RAY DIFFRACTION	3.07
1.83-1.85	0.3645	14	0.2591	299	X-RAY DIFFRACTION	5.84
1.85-1.87	0.2903	31	0.2742	606	X-RAY DIFFRACTION	11.88
1.87-1.89	0.285	49	0.2595	954	X-RAY DIFFRACTION	18.76
1.89-1.92	0.2764	64	0.2551	1249	X-RAY DIFFRACTION	24.23
1.92-1.95	0.3453	64	0.2664	1513	X-RAY DIFFRACTION	29.59
1.95-1.97	0.3308	97	0.2643	1720	X-RAY DIFFRACTION	33.65
1.97-2	0.31	97	0.263	2004	X-RAY DIFFRACTION	39.23
2-2.03	0.3061	127	0.2563	2256	X-RAY DIFFRACTION	44.18
2.03-2.07	0.2653	144	0.2528	2646	X-RAY DIFFRACTION	52.17
2.07-2.1	0.3032	144	0.2494	2978	X-RAY DIFFRACTION	58.08
2.1-2.14	0.2595	189	0.2475	3352	X-RAY DIFFRACTION	65.38
2.14-2.18	0.295	183	0.2367	3660	X-RAY DIFFRACTION	72.02
2.18-2.23	0.2915	234	0.2383	4079	X-RAY DIFFRACTION	79.12
2.23-2.28	0.292	237	0.2193	4303	X-RAY DIFFRACTION	85.29
2.28-2.33	0.2633	263	0.2055	4731	X-RAY DIFFRACTION	93.05
2.33-2.39	0.2644	266	0.2107	5026	X-RAY DIFFRACTION	97.14
2.39-2.45	0.2828	278	0.2176	5066	X-RAY DIFFRACTION	99.85
2.45-2.52	0.2882	268	0.2123	5108	X-RAY DIFFRACTION	99.96
2.52-2.61	0.2472	291	0.2131	5108	X-RAY DIFFRACTION	99.91
2.61-2.7	0.2435	266	0.2076	5118	X-RAY DIFFRACTION	99.93
2.7-2.81	0.2709	257	0.2082	5146	X-RAY DIFFRACTION	99.98
2.81-2.93	0.2618	272	0.2003	5111	X-RAY DIFFRACTION	99.98
2.93-3.09	0.2532	282	0.1927	5120	X-RAY DIFFRACTION	99.98
3.09-3.28	0.2184	258	0.1797	5148	X-RAY DIFFRACTION	99.98
3.28-3.54	0.2135	275	0.173	5160	X-RAY DIFFRACTION	99.98
3.54-3.89	0.1851	277	0.1503	5115	X-RAY DIFFRACTION	99.87
3.89-4.46	0.1655	271	0.1391	5167	X-RAY DIFFRACTION	100
4.46-5.61	0.1828	247	0.1452	5190	X-RAY DIFFRACTION	99.91
5.61-119.06	0.1961	257	0.1611	5260	X-RAY DIFFRACTION	99.91

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	0.0495723418398	-0.0157838830394	-0.0576655205826	0.0621484750794	-0.0100767701867	0.0850480893686	-0.123793929371	0.0215714524307	-0.10850879863	0.134256517476	0.015780838343	0.0141406858958	0.257043608081	-0.0559095326177	-0.149780399284	0.331164986882	-0.0557314094016	0.0845271463794	0.114100551494	-0.0241099651844	0.159526846959	3.4427793005	-54.5168125093	27.8154343092
2	0.00134690738673	-0.00203898025094	0.0071573937942	0.00791107071538	-0.00782076231274	0.0251613497936	-0.0155405277045	-0.0213911685221	-0.00577353048115	0.0399966124333	0.00759337036826	0.00139498046026	0.0509125794776	0.0185056328996	-0.00185796101351	0.337549668978	0.0853090422318	0.0419961562522	0.117713648323	0.0227283222553	0.154728856571	23.4465781796	-61.1486726471	32.5658662537
3	0.000986611823692	-0.000788935480778	-0.0023755235347	0.00667520001798	0.010300997107	0.0137684317403	0.0129900378424	-0.00912322293251	0.00234139145213	0.0352728719564	-0.0529190450702	0.0057811771465	0.0335527031203	-0.0479219539412	-2.89985176788E-6	0.262183588654	-0.00883521191922	0.0144441805071	0.155649662002	-0.0242459004659	0.139546768659	2.67306652741	-29.0953781516	42.8039181249
4	-1.12014649356E-5	-0.00067949050264	-0.000303340115646	0.00160043915872	0.00143082380364	0.00289087806932	0.0144481511431	-0.00589849970244	-0.021422468594	0.001172793108	-0.000901475701934	-0.00633849444707	-0.00819928277228	0.00322119287031	3.98617760572E-6	0.362492888992	-0.0713333470797	0.0307180619856	0.197221129367	0.0179306145553	0.136356397392	1.29140805808	-50.5348892597	61.0713992237
5	0.0124608449177	0.0144763638615	-0.00378626502375	0.0194075898011	-0.00457053635693	0.00319603659745	0.0619089687476	-0.0790595510831	0.00818883469408	0.125721134748	-0.0542563841884	0.0290436907918	0.0359000896573	-0.0195022618043	0.00354762041811	0.407793596301	-0.0430572919347	0.0396258918759	0.178568129315	-0.00700579152873	0.0960881657066	2.64046379157	-33.6403459351	60.5045129916
6	0.019983424873	-0.0119684626286	0.0136635947127	0.00742436495839	-0.00854037131559	0.00960119263087	-0.0113218697381	-0.0073745244426	-0.00645829984386	0.0103096554672	-0.0392831257012	0.021664660717	0.0228080520779	-0.0325539606355	-0.00488464584667	0.350414693495	-0.0219178180249	0.109639549468	0.172815189597	-0.0555038645165	0.183249824967	-14.156838404	-23.1952763102	51.5069342168
7	0.00054279954343	0.000516985752654	-0.000390370580651	0.000391339831361	-0.000311146126972	0.000196210793473	-0.00211078844917	-0.00141015909884	-0.0014729891619	-0.00458675611578	0.00261582019764	0.00153077943273	0.00513331870031	-0.00297188781708	-8.63717415138E-8	0.583843813739	-0.0317548641975	0.0623205614605	0.575989840001	-0.0159456703422	0.567142004628	-24.6541886853	-35.3518110243	48.584851696
8	0.00425629668875	-0.00846694116952	-0.00467194766061	0.0162638627647	0.00806797667376	0.0035346581838	0.00942973049805	0.0426697202729	-0.0227329184616	0.00697000790984	-0.0578929826337	0.00880650818467	-0.00566934642843	-0.0199623746478	-0.0152690920029	0.117728302154	0.0235320075159	-0.0560596903245	0.15867292717	-0.0234308803801	0.125048298971	17.0988241202	-29.4599708554	11.9677303424
9	0.0163895455872	-0.00438603873065	0.00083235411751	0.0064461881927	0.000637373006798	0.0237266956124	0.00725455875494	0.00816668412128	0.00830601284349	0.017832779831	-0.00793857437215	-0.0345816389527	-0.0016355930667	0.00271861100461	0.0221938531983	0.064117767074	-0.00303634289434	-0.0837621539322	0.149389919167	0.0183567411112	0.19876752305	35.8016014656	-8.19404521133	17.7856865692
10	0.0123045733521	-0.0144965705238	-0.00877453523626	0.0167080466248	0.0103714727962	0.00614147418577	0.0111185063502	0.0284573870169	-0.0100207484468	-0.0107283316716	0.0128384256086	-0.0287151048062	-0.00113556247437	0.00810092689477	0.0162432380761	0.054221102152	0.0110887477427	0.0125480700314	0.180390789719	0.0386695080914	0.268632632239	43.6498412658	-14.523315578	1.97521926599
11	0.00164701045043	0.00189286751742	0.00201563712908	0.0243468547049	0.0146255729018	0.00692498865282	-0.00450349434474	0.00788473726469	0.0429397771527	0.0314847668228	0.00165271650003	-0.101158969216	0.0034585205776	0.0085135492078	-0.0394900251271	0.0329813952839	0.0180665003906	-0.106502024774	0.148075533734	-0.000643469217365	0.24653821029	37.1948027446	-20.9856070989	16.7703888335
12	0.00130799276862	-0.000190013304482	-0.00115270301535	-5.66482012843E-5	0.000197258070995	0.000918212760867	0.00974285735951	0.00659171065726	-0.00563483818414	-0.0286944354899	0.00188550793248	-0.0258880545725	-0.00645269300937	-0.00129644359561	-9.77612075936E-8	0.151063031975	0.0643210683709	0.0706774925891	0.181956678843	0.0108226471694	0.195103995846	31.4493390258	-30.5815955417	-7.1683723092
13	0.00257146275137	-0.000577622979104	0.000621034615298	0.00065726238842	0.00117887028527	0.00214232679407	0.0443589920433	0.0352232945106	0.0202560640054	-0.0507487913977	-0.0245530201192	-0.0376276134923	-0.00501712760533	0.000405902872275	0.00170688874897	0.126795534419	0.0481680940735	0.017634148234	0.155947868153	0.00149823916758	0.153005379913	24.5286662171	-28.3195442256	-2.84850686826
14	0.000122053807659	-0.000202896112683	5.83980118173E-5	0.000752998108908	-0.00124174977819	0.00256950140143	0.00882031484165	-0.00432177934636	0.00666278024143	-0.0057331153861	0.0050690424716	0.00144176588395	0.00347951565423	0.00798558395	2.58219872208E-6	0.374396900242	0.0524759238346	0.015485179719	0.346651575045	0.0238767119319	0.294090463767	18.2621363949	-22.3899993752	-11.691706137
15	0.00970321372801	-0.0123483495235	-0.0140264882558	0.0931194063377	0.0090482031981	0.051770027633	-0.00222377846862	0.0744613645407	0.11944774159	0.0470248689044	0.0159217854818	-0.00836029760755	-0.0338590724869	-0.00965127670108	0.0547776233655	-0.00438968018803	-0.00248874657886	-0.0393972239684	0.11627447889	0.000978357551714	0.153306652287	7.44770516401	0.372469797174	21.7584004624
16	0.00214217964594	0.00439491327972	0.0010660404272	0.00725583387099	0.000629746557415	0.00521727314233	0.00540208545411	-0.00527647865105	0.0840517561383	0.0308278744004	0.0216342323164	-0.0821811169082	0.0155743342275	0.00403205569053	0.00166093123346	0.188768192635	0.00513024658219	-0.00384923808122	0.0885268103066	-0.0372708887755	0.212541410821	18.0618656106	7.61651385915	38.2697350352

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 2 through 371 )	A	A	2 - 371	1 - 370
2	2	chain 'A' and (resid 372 through 466 )	A	A	372 - 466	371 - 460
3	3	chain 'B' and (resid 2 through 99 )	B	E	2 - 99	1 - 98
4	4	chain 'B' and (resid 100 through 132 )	B	E	100 - 132	99 - 131
5	5	chain 'B' and (resid 133 through 371 )	B	E	133 - 371	132 - 370
6	6	chain 'B' and (resid 372 through 441 )	B	E	372 - 441	371 - 433
7	7	chain 'B' and (resid 442 through 466 )	B	E	442 - 466	434 - 458
8	8	chain 'C' and (resid 2 through 75 )	C	H	2 - 75	1 - 74
9	9	chain 'C' and (resid 76 through 132 )	C	H	76 - 132	75 - 131
10	10	chain 'C' and (resid 133 through 190 )	C	H	133 - 190	132 - 189
11	11	chain 'C' and (resid 191 through 342 )	C	H	191 - 342	190 - 341
12	12	chain 'C' and (resid 343 through 371 )	C	H	343 - 371	342 - 370
13	13	chain 'C' and (resid 372 through 437 )	C	H	372 - 437	371 - 436
14	14	chain 'C' and (resid 438 through 466 )	C	H	438 - 466	437 - 465
15	15	chain 'D' and (resid 2 through 371 )	D	M	2 - 371	1 - 370
16	16	chain 'D' and (resid 372 through 467 )	D	M	372 - 467	371 - 462

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 1088 molecules

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 1088 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi