PDB-4r33: X-ray structure of the tryptophan lyase NosL with Tryptophan and ...

ID or keywords:

Entry

Database: PDB / ID: 4r33

Title

X-ray structure of the tryptophan lyase NosL with Tryptophan and S-adenosyl-L-homocysteine bound

Components

NosL

Keywords

LYASE / Radical SAM enzyme/beta-alpha barrel / tryptophan lyase / Fe4S4 cluster and S-adenosyl-L-methionine

Function / homology

Function and homology information

4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function

Biological species

Streptomyces actuosus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Nicolet, Y. / Zeppieri, L. / Amara, P. / Fontecilla-Camps, J.-C.

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Crystal Structure of Tryptophan Lyase (NosL): Evidence for Radical Formation at the Amino Group of Tryptophan.
Authors: Nicolet, Y. / Zeppieri, L. / Amara, P. / Fontecilla-Camps, J.C.

History

Deposition	Aug 14, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 12, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4r33.cif.gz	339.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4r33.ent.gz	275.2 KB	Display	PDB format
PDBx/mmJSON format	4r33.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4r33_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4r33_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4r33_validation.xml.gz	36.8 KB	Display
Data in CIF	4r33_validation.cif.gz	56 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r3/4r33 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/4r33	HTTPS FTP

-
Related structure data

Related structure data	4r34C C: citing same article (ref.)
Similar structure data	4r34-1 6htm-2 6hto-d 6htk-1 4r34-2 6htm-1 6htk-2 6mm8-d 7ajk-d 5oth-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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: NosL

B: NosL

hetero molecules

96.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NosL

hetero molecules

A: NosL

hetero molecules

defined by author&software
95.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NosL

hetero molecules

B: NosL

hetero molecules

defined by author&software
96.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.720, 47.230, 114.360
Angle α, β, γ (deg.)	90.00, 108.71, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	A-666- HOH
2	1	B-745- HOH
3	1	B-767- HOH
4	1	B-789- HOH
5	1	B-1041- HOH

-
Protein , 1 types, 2 molecules AB

#1: Protein	NosL Mass: 46833.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces actuosus (bacteria) / Strain: Streptomyces actuosus / Gene: nosL / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: C6FX51

-
Non-polymers , 8 types, 756 molecules

#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄
#4: Chemical	ChemComp-TRP / TRYPTOPHAN Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.11 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 14-20% PEG 3350; 200 mM KBr; 1 mM Tryptophan; 15 mg/mL protein, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 15, 2014
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 1.78→47.23 Å / Num. all: 180436 / Num. obs: 179387 / % possible obs: 0.996 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 1.78→1.89 Å / % possible all: 0.983

-
Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.78→47.23 Å / SU ML: 0.19 / σ(F): 1.16 / Phase error: 18.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1813	8974	5 %
R_work	0.1586	-	-
obs	0.1597	179387	99.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.78→47.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5980	0	127	741	6848

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6361
X-RAY DIFFRACTION	f_angle_d	1.156	8659
X-RAY DIFFRACTION	f_dihedral_angle_d	13.504	2379
X-RAY DIFFRACTION	f_chiral_restr	0.062	949
X-RAY DIFFRACTION	f_plane_restr	0.005	1140

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 (%)
1.78-1.8002	0.3192	284	0.2924	5580	X-RAY DIFFRACTION	97
1.8002-1.8214	0.2664	310	0.2685	5779	X-RAY DIFFRACTION	100
1.8214-1.8436	0.2814	294	0.2579	5527	X-RAY DIFFRACTION	100
1.8436-1.8669	0.2604	303	0.2465	5698	X-RAY DIFFRACTION	100
1.8669-1.8915	0.2807	307	0.2292	5849	X-RAY DIFFRACTION	100
1.8915-1.9174	0.2512	285	0.2288	5535	X-RAY DIFFRACTION	100
1.9174-1.9448	0.2524	301	0.2142	5757	X-RAY DIFFRACTION	100
1.9448-1.9738	0.226	301	0.2142	5739	X-RAY DIFFRACTION	100
1.9738-2.0047	0.2507	297	0.2009	5592	X-RAY DIFFRACTION	100
2.0047-2.0375	0.2291	301	0.2065	5701	X-RAY DIFFRACTION	100
2.0375-2.0727	0.2016	299	0.1852	5651	X-RAY DIFFRACTION	100
2.0727-2.1104	0.1986	294	0.1739	5675	X-RAY DIFFRACTION	100
2.1104-2.151	0.1977	303	0.1763	5792	X-RAY DIFFRACTION	100
2.151-2.1949	0.2079	300	0.1652	5595	X-RAY DIFFRACTION	100
2.1949-2.2426	0.1763	307	0.1614	5741	X-RAY DIFFRACTION	100
2.2426-2.2948	0.1968	300	0.1552	5632	X-RAY DIFFRACTION	100
2.2948-2.3521	0.2163	304	0.1591	5769	X-RAY DIFFRACTION	100
2.3521-2.4157	0.1737	302	0.1627	5596	X-RAY DIFFRACTION	100
2.4157-2.4868	0.1953	304	0.1556	5747	X-RAY DIFFRACTION	100
2.4868-2.5671	0.165	295	0.1472	5641	X-RAY DIFFRACTION	100
2.5671-2.6588	0.1602	299	0.1518	5666	X-RAY DIFFRACTION	100
2.6588-2.7653	0.2304	297	0.1545	5698	X-RAY DIFFRACTION	100
2.7653-2.8911	0.1688	295	0.1492	5676	X-RAY DIFFRACTION	100
2.8911-3.0435	0.1616	299	0.1422	5705	X-RAY DIFFRACTION	100
3.0435-3.2341	0.1733	298	0.1483	5652	X-RAY DIFFRACTION	100
3.2341-3.4838	0.1595	301	0.1383	5689	X-RAY DIFFRACTION	100
3.4838-3.8342	0.1284	298	0.1334	5698	X-RAY DIFFRACTION	100
3.8342-4.3887	0.145	295	0.1238	5702	X-RAY DIFFRACTION	100
4.3887-5.528	0.1485	301	0.1278	5664	X-RAY DIFFRACTION	99
5.528-47.2466	0.1675	300	0.1508	5667	X-RAY DIFFRACTION	99

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	0.2679	-0.2334	-0.4291	0.3426	0.4104	2.8561	0.4584	-0.4127	0.1355	0.2455	-0.1445	-0.4906	-0.3504	0.8415	-0.3159	0.5349	-0.3309	0.0013	0.7449	-0.1235	0.4887	70.5482	63.2144	39.0793
2	3.4897	1.9419	-2.2755	1.9013	-1.1174	2.3589	-0.0447	-0.0155	-0.3611	0.0392	0.0869	-0.4545	-0.0712	0.37	-0.0756	0.3024	-0.0056	-0.0058	0.3913	-0.0594	0.2767	60.0499	49.9829	31.7062
3	0.8718	0.1168	-0.5933	0.6235	0.0863	1.27	0.2681	0.0315	0.2011	0.0316	-0.051	0.0595	-0.4909	-0.1179	-0.1757	0.4209	0.0383	0.0813	0.2228	0.0338	0.1769	33.2829	57.0771	43.9258
4	1.9343	0.0899	-1.059	2.5099	1.394	3.2469	0.2458	-0.4017	0.033	0.2933	-0.0708	-0.1832	-0.2954	0.4108	-0.1727	0.3872	-0.0421	0.0019	0.3034	0.0073	0.1475	43.003	52.2997	52.1881
5	1.6147	0.2034	-0.4035	1.2541	0.4702	1.6995	0.4761	-0.3825	0.3722	0.2617	-0.1118	-0.1423	-0.7912	0.5674	-0.3681	0.6044	-0.1812	0.1273	0.3764	-0.086	0.2946	51.8699	66.5819	46.8816
6	2.0142	0.2962	-0.6807	1.1734	0.4337	1.4785	0.2791	0.0031	0.2078	-0.0516	0.007	-0.1161	-0.5723	0.174	-0.271	0.415	-0.0476	0.0849	0.2632	-0.0228	0.1925	51.7087	60.0417	32.2004
7	1.3052	0.1448	-0.2737	3.0481	0.3554	2.1683	0.2795	0.3961	0.2846	-0.3575	-0.0448	0.161	-0.4307	-0.3943	-0.2058	0.4532	0.1351	0.0668	0.3151	0.0686	0.2079	31.4206	57.7829	30.5628
8	1.8422	-0.447	-0.8238	1.9324	0.8739	3.133	0.1259	0.1864	-0.1166	-0.0566	0.026	0.0403	-0.0995	-0.029	-0.1241	0.2444	0.0078	-0.0043	0.2348	0.0404	0.1473	42.2634	47.7192	29.9909
9	6.1661	0.3715	1.3498	1.5451	-0.2145	2.0381	0.0793	-0.5009	-0.2819	0.2352	0.1308	0.3847	-0.113	-0.4124	-0.187	0.2174	-0.0123	0.0444	0.3599	0.1097	0.2752	9.6835	36.5579	18.8658
10	1.7943	0.0351	0.0945	0.7201	-0.2513	0.5476	-0.0419	-0.0202	-0.0403	-0.0088	0.0282	0.0291	-0.0181	-0.0266	0.0231	0.0942	-0.0034	-0.0242	0.1325	-0.0207	0.1244	32.491	45.6704	0.424
11	2.7063	0.1481	0.3586	1.5005	0.4066	1.9984	0.0325	-0.2065	-0.4963	0.1019	-0.0183	0.0215	0.2019	-0.0399	-0.0045	0.1249	0.004	-0.001	0.1705	0.0514	0.2198	28.1283	33.037	9.6767
12	1.8041	0.0425	0.1295	0.7569	-0.161	1.0217	-0.0212	-0.009	-0.1932	-0.0162	0.0687	0.1921	0.062	-0.1304	-0.0339	0.1097	-0.0099	-0.0179	0.1715	0.0079	0.2253	16.2332	40.0081	3.1196
13	1.8205	-0.622	0.3715	1.8395	-0.479	1.041	-0.034	0.2503	0.0251	-0.2017	0.0501	0.1891	-0.0192	-0.0972	-0.0163	0.1246	-0.0294	-0.0421	0.2044	-0.0034	0.1778	23.5222	48.149	-9.8137

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 64 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 65 through 86 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 87 through 167 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 168 through 200 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 201 through 273 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 274 through 345 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 346 through 365 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 366 through 501 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 10 through 64 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 65 through 200 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 201 through 256 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 257 through 345 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 346 through 501 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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, 2 molecules AB

-
Non-polymers , 8 types, 756 molecules

-
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

-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, 2 molecules AB

-Non-polymers , 8 types, 756 molecules

-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

-
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, 2 molecules AB

-
Non-polymers , 8 types, 756 molecules

-
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