PDB-8v6p: Proteus vulgaris tryptophan indole-lyase complexed with 7-aza-L-t...

ID or keywords:

Entry

Database: PDB / ID: 8v6p

Title

Proteus vulgaris tryptophan indole-lyase complexed with 7-aza-L-tryptophan

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: 1.74 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	Dec 2, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 31, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8v6p.cif.gz	976.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8v6p.ent.gz		Display	PDB format
PDBx/mmJSON format	8v6p.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/v6/8v6p ftp://data.pdbj.org/pub/pdb/validation_reports/v6/8v6p	HTTPS FTP

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Related structure data

Related structure data	8v2kC 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)	151.635, 211.340, 60.956
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

Components on special symmetry positions

ID	Model	Components
1	1	C-975- HOH

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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, 1389 molecules

#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-A1ACN / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-3-(1H-pyrrolo[2,3-b]pyridin-3-yl)-L-alanine Mass: 434.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₁₉N₄O₇P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-A1ABZ / (2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-3-(1H-pyrrolo[2,3-b]pyridin-3-yl)propanoic acid Mass: 434.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₁₉N₄O₇P / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1382 / 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: 2.32 Å³/Da / Density % sol: 47.05 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M potassium phosphate, pH 8.0, 1 mM DTT, 0.1 mM PLP, 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: Nov 19, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.74→61.6 Å / Num. obs: 137266 / % possible obs: 93.6 % / Redundancy: 6.9 % / B_iso Wilson estimate: 21.22 Å² / CC_1/2: 0.992 / Net I/σ(I): 5.6
Reflection shell	Resolution: 1.74→1.92 Å / Num. unique obs: 6863 / CC_1/2: 0.59

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
autoPROC	20230614	data processing
XDS		data reduction
STARANISO		data scaling
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.74→61.6 Å / SU ML: 0.2094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3558
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2279	6816	4.97 %
R_work	0.1851	130367	-
obs	0.1873	137183	67.93 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.57 Å²

Refinement step

Cycle: LAST / Resolution: 1.74→61.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14681	0	126	1385	16192

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0047	16343
X-RAY DIFFRACTION	f_angle_d	0.723	22130
X-RAY DIFFRACTION	f_chiral_restr	0.0491	2371
X-RAY DIFFRACTION	f_plane_restr	0.0064	2881
X-RAY DIFFRACTION	f_dihedral_angle_d	13.2994	6176

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 (%)
1.74-1.76	0.2912	11	0.3325	252	X-RAY DIFFRACTION	3.96
1.76-1.78	0.4398	23	0.3066	329	X-RAY DIFFRACTION	5.35
1.78-1.8	0.4166	23	0.2977	463	X-RAY DIFFRACTION	7.27
1.8-1.82	0.3638	35	0.271	561	X-RAY DIFFRACTION	9.05
1.82-1.85	0.2275	37	0.2479	690	X-RAY DIFFRACTION	10.83
1.85-1.87	0.3188	42	0.2425	965	X-RAY DIFFRACTION	15.12
1.87-1.9	0.339	75	0.2426	1343	X-RAY DIFFRACTION	21.33
1.9-1.93	0.3342	105	0.2444	2049	X-RAY DIFFRACTION	32.21
1.93-1.96	0.3001	128	0.249	2530	X-RAY DIFFRACTION	40.02
1.96-1.99	0.2713	164	0.24	2852	X-RAY DIFFRACTION	45.34
1.99-2.02	0.2852	174	0.2239	3300	X-RAY DIFFRACTION	51.57
2.02-2.06	0.278	211	0.2221	3691	X-RAY DIFFRACTION	58.88
2.06-2.1	0.2367	215	0.2237	4365	X-RAY DIFFRACTION	68
2.1-2.14	0.2857	271	0.2245	4933	X-RAY DIFFRACTION	78.49
2.14-2.19	0.2436	266	0.2252	5668	X-RAY DIFFRACTION	88.16
2.19-2.24	0.2827	311	0.2204	6123	X-RAY DIFFRACTION	95.83
2.24-2.3	0.2653	326	0.2227	6264	X-RAY DIFFRACTION	98.77
2.3-2.36	0.2541	372	0.2181	6316	X-RAY DIFFRACTION	99.67
2.36-2.43	0.2738	349	0.2135	6359	X-RAY DIFFRACTION	99.64
2.43-2.51	0.2527	331	0.206	6361	X-RAY DIFFRACTION	100
2.51-2.6	0.2682	313	0.2031	6412	X-RAY DIFFRACTION	100
2.6-2.7	0.2417	326	0.196	6423	X-RAY DIFFRACTION	99.99
2.7-2.82	0.2604	326	0.2005	6434	X-RAY DIFFRACTION	100
2.82-2.97	0.2315	321	0.1968	6451	X-RAY DIFFRACTION	99.94
2.97-3.16	0.2342	326	0.1958	6421	X-RAY DIFFRACTION	99.99
3.16-3.4	0.2146	345	0.1723	6445	X-RAY DIFFRACTION	99.82
3.4-3.74	0.2112	361	0.1576	6442	X-RAY DIFFRACTION	99.88
3.74-4.28	0.1774	332	0.1417	6507	X-RAY DIFFRACTION	99.99
4.28-5.4	0.1769	352	0.1378	6586	X-RAY DIFFRACTION	100
5.4-61.6	0.1952	345	0.1754	6832	X-RAY DIFFRACTION	99.5

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	2.93816956244	-0.555251242675	-0.0444549948542	0.731088588225	-0.452563689243	0.334750353967	-0.129908597644	-0.731703817664	0.289070928134	0.302466668811	0.0117826583344	0.502704147273	-0.0370627354113	-0.160641802629	-0.605429793168	0.102049961384	0.0248895968894	0.158205697576	0.343354449769	-0.113233958273	0.682466213067	-8.3583690528	23.8879678056	21.1436916909
2	1.29818702255	0.482531563619	0.0858119088165	0.705924058951	0.465933334445	1.23234491411	-0.155750006188	-0.492435447075	0.354962066205	0.358459253594	-0.252310440952	1.07278334031	-0.0996621161212	-0.484785873807	-0.230726453271	0.0723714393375	-0.0332104031779	0.232280064449	0.244096055483	-0.0900584114664	0.684556600079	-0.379979946317	25.6894443494	23.2307992784
3	0.740767277121	0.198590077338	0.864667812983	0.0531300725807	0.233367066495	1.01289161503	-0.021221518739	-0.853531897433	0.606520071935	0.711336993194	-0.154778392711	0.686740582092	-0.0497987515958	-0.612222659385	-0.0875111761553	0.601292693748	-0.0468283573255	0.413058471662	0.777508561463	-0.298852705391	1.22929376339	-2.85058991528	30.4991423258	33.9889349167
4	1.03507188274	0.122161665462	-0.126492566233	0.850739653568	-0.460547841884	0.422687328368	0.0862183317205	-0.552387986301	0.149719015852	0.43708926326	-0.326325199734	-0.179937597466	-0.0852308282352	0.112984853446	-0.0955688608994	0.238853641633	-0.0987832593658	-0.0618401895642	0.28879802357	0.0891655263179	0.0816715993322	52.3022506117	27.1640738204	17.4943776628
5	1.96987410944	-0.197899044676	0.364465735614	0.994368837419	-0.221453164009	0.859417617398	0.0227193783425	0.124946056715	-0.257272712215	-0.260265264194	-0.0811449488491	-0.465074306269	-0.039374630084	0.0545949468962	0.0336720781218	0.139159627151	0.0227284782961	0.109621307756	0.114206081223	0.021277997793	0.204990570018	54.0964552186	9.87277047987	-6.57059781703
6	0.763648744256	0.299422494084	0.0716987418906	1.08305838454	0.0722369842292	0.328409635646	0.0955747280061	0.15617654155	-0.0698618265358	-0.0818694364366	-0.0629325277203	-0.795522260525	0.0348888671495	0.0970679818909	0.0109160877061	0.108934837663	0.0329025938422	0.235367614733	0.187638171968	0.127522239615	0.147463679353	58.2474162487	21.2181638036	-7.30752040307
7	0.325467770522	0.441113884975	-0.0632559059808	1.52794549265	-0.192085997921	1.12796851768	0.059045738676	-0.245606246319	-0.0535210455084	0.129677566225	-0.309834024096	-1.0522197607	0.150254052097	0.539522178102	-0.00863593427851	0.160439230853	-0.0327565281475	-0.0611186745723	0.36049226217	0.17201497849	0.496529087789	70.2808033938	25.3873069901	12.5807446478
8	0.142839149923	0.121658219143	-0.277928500765	0.995123722696	-0.720394527686	0.809268221294	-0.0794342290172	-0.540084900566	-0.54707965301	0.472775346478	-0.119263686382	-0.647695466734	-0.0778958914303	0.467373349002	0.221401886218	0.30399142383	-0.0336985432379	-0.108970621574	0.530812608618	0.221284316406	0.830502273381	69.7407002868	22.1418709629	20.0192456907
9	1.34820653142	0.134408336488	-0.0993548879654	1.61757269166	-0.211520578885	0.617917972158	0.0314154816646	0.113018239245	-0.03395606168	-0.0853659405555	-0.0427716477332	0.0721800683114	0.0906102229479	0.0174198265416	-0.00288042655909	0.132358682957	-0.0138973207695	-0.00622681062371	0.0713061618843	0.00521758345081	0.0179587096759	31.3948702323	10.5750951704	9.48222637408
10	1.28769107794	-1.33021561155	0.15465966324	1.37790277504	-0.168893742423	1.09833993635	0.00201835397581	-0.0217021452911	-0.309733344023	0.158421113355	-0.111913349684	-0.487225493602	0.00467176077863	0.212023613081	0.0334224194849	0.125911236287	0.0206561736832	-0.0360386595863	0.134317565135	0.0923009768687	0.299835287634	47.3395927571	-10.6950300013	11.2546441129
11	0.785594096877	0.10823635834	-0.136267950677	1.50397271332	-0.186756644104	0.557723482422	0.0984913860972	-0.144113683235	-0.293209189653	0.321036359762	-0.196849809466	0.0740277334436	0.0693797024493	0.060680217466	-0.0414312858451	0.136607860727	-0.0074686152202	-0.0172815422852	0.0762879136883	0.0883127165587	0.131907089105	34.4655630046	-4.98602926355	17.5376397279
12	1.68032800351	-0.0487523810811	-0.300847010894	1.53705732462	-0.365104072957	2.24027393599	-0.231069566565	0.56017800373	-0.881709982349	-0.946178505635	-0.0881716933877	0.132428721203	0.838312547584	0.198974745956	-0.127553953134	0.425803832501	-0.0797002079267	0.0838441821434	0.179757523424	-0.144790866158	0.414344985042	26.6469722334	-5.88370793575	-2.89795495927
13	1.14618732616	0.0197241115159	0.232475665366	1.87190062208	-0.0885799571219	0.924399158243	-0.0419800157804	0.291320652291	0.324991695863	-0.161369439496	0.0315088162181	-0.0688319956728	-0.116885967271	0.0465174677988	-0.028654883409	0.128084753858	-0.021894441835	0.0174496317025	0.171632677117	0.0556781382961	0.127786716871	36.1847439852	44.1381179185	8.44624568049
14	0.913476683803	-0.238301152392	-0.12361193382	1.41310991543	0.157298191647	0.61342051046	-0.124271663089	-0.474685307081	0.401276185454	0.26333716866	-0.00383631087747	-0.047751225908	-0.126913648241	-0.0102839940666	-0.0024787473274	0.316407291038	0.0277268351571	-0.0515819404438	0.263695797199	-0.207480635396	0.257791684913	26.5609458534	55.5609329967	31.3055340659
15	1.39027268365	0.348281141306	0.120014418285	0.944034884316	0.279226626256	0.42231496934	-0.0163011011293	-0.0226655865246	0.863297163335	0.0746388713951	0.00991655948442	0.0849585843974	-0.255582514473	-0.0418279787468	-0.0444191679935	0.238702284973	-0.0291630341014	-0.000164100765876	0.128790336605	-0.00398345476952	0.461106129763	36.4734831865	58.4437308481	12.1206709809
16	1.17180470757	-0.226073506186	-0.0167488448562	0.319097968422	-0.11008287244	1.04493294053	0.0148950261932	-0.552231430332	-0.159104851312	0.558964162748	-0.107231592961	0.459162575667	0.0882133040995	-0.375599855229	0.0465198970922	0.347275712953	-0.0608177875376	0.251067231066	0.348537382449	0.0176280650094	0.22538669599	12.3333049554	19.5726386961	24.4628267258
17	1.08237798657	-0.060886603408	-0.540411843036	1.88305596561	-0.448002532229	0.671914678051	0.0264052623877	0.10279956766	-0.0958652607595	-0.0481063477405	-0.0497620822227	0.0655282725418	-0.0256524008405	-0.00199115018758	0.0274036773173	0.0713193431619	0.00726895851145	0.0108856919924	0.0856072135557	0.0224999569538	0.055986565617	19.0971070705	36.3824479839	5.80480112787
18	1.95853588581	-0.0616694184817	0.302053443474	0.00485249508013	-0.0155137619306	0.851626227574	-0.0605714097201	0.0994948515423	0.0529569863466	0.241200175603	0.0746618053365	0.340245720524	-0.0880054577448	-0.0545785063002	-0.00614338921291	0.126738330557	0.0314028255437	0.0270619169079	0.0985454351857	0.00130158951697	0.283136209876	-2.08916714955	48.714758265	12.1021687734
19	0.885210429198	0.0526037333198	-0.110602902217	0.821703349333	0.0348595375415	0.434309036818	-0.0760646231971	0.247849558999	-0.0816268915865	-0.0945724992763	0.0502311671773	0.436242344248	-0.122551663656	0.00933940207676	0.00713380850767	0.04579122682	0.0506960848196	-0.0224788941254	0.0582295755737	0.000800340307682	0.248963210928	2.44703132296	36.3091718707	3.65635538291

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 'B' and (resid 343 through 371 )	B	F	343 - 371	342 - 370
2	2	chain 'B' and (resid 372 through 437 )	B	F	372 - 437	371 - 436
3	3	chain 'B' and (resid 438 through 467 )	B	F	438 - 467	437 - 466
4	4	chain 'C' and (resid 2 through 75 )	C	H	2 - 75	1 - 74
5	5	chain 'C' and (resid 76 through 141 )	C	H	76 - 141	75 - 140
6	6	chain 'C' and (resid 142 through 341 )	C	H	142 - 341	141 - 340
7	7	chain 'C' and (resid 342 through 423 )	C	H	342 - 423	341 - 415
8	8	chain 'C' and (resid 424 through 466 )	C	H	424 - 466	416 - 458
9	9	chain 'D' and (resid 2 through 99 )	D	J	2 - 99	1 - 98
10	10	chain 'D' and (resid 100 through 155 )	D	J	100 - 155	99 - 154
11	11	chain 'D' and (resid 156 through 371 )	D	J	156 - 371	155 - 370
12	12	chain 'D' and (resid 372 through 466 )	D	J	372 - 466	371 - 465
13	13	chain 'A' and (resid 2 through 75 )	A	A	2 - 75	1 - 74
14	14	chain 'A' and (resid 76 through 295 )	A	A	76 - 295	75 - 294
15	15	chain 'A' and (resid 296 through 466 )	A	A	296 - 466	295 - 465
16	16	chain 'B' and (resid 2 through 43 )	B	F	2 - 43	1 - 42
17	17	chain 'B' and (resid 44 through 99 )	B	F	44 - 99	43 - 98
18	18	chain 'B' and (resid 100 through 155 )	B	F	100 - 155	99 - 154
19	19	chain 'B' and (resid 156 through 342 )	B	F	156 - 342	155 - 341

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