PDB-5g3s: The structure of the L-tryptophan oxidase VioA from Chromobacteri...

ID or keywords:

Entry

Database: PDB / ID: 5g3s

Title

The structure of the L-tryptophan oxidase VioA from Chromobacterium violaceum - Samarium derivative

Components

L-TRYPTOPHAN OXIDASE VIOA

Keywords

OXIDOREDUCTASE / VIOLACEIN / L-TRYPTOPHAN OXIDASE / FLAVOENZYME / SAMARIUM DERIVATIVE

Function / homology

Function and homology information

7-chloro-L-tryptophan oxidase / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function

Biological species

CHROMOBACTERIUM VIOLACEUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.076 Å

Authors

Krausze, J. / Rabe, J. / Moser, J.

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Biosynthesis of Violacein: Structure and Function of L-Tryptophan Oxidase Vioa Chromobacterium Violaceum
Authors: Fuller, J. / Roepke, R. / Krausze, J. / Rennhack, K.E. / Daniel, N.P. / Blankenfeldt, W. / Schulz, S. / Jahn, D. / Moser, J.

History

Deposition	May 1, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 10, 2016	Group: Database references
Revision 1.2	Oct 5, 2016	Group: Database references
Revision 1.3	Mar 6, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5g3s.cif.gz	479.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g3/5g3s ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g3s	HTTPS FTP

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Related structure data

Related structure data	5g3tC 5g3uC C: citing same article (ref.)
Similar structure data	6g2p-d 5g3u-d 5zbc-d 5zbd-d 6esd-d 5g3t-2 6fw7-d 6fw9-d 2bry-d 4kip-d Search similar-shape structures by Omokage search (details) 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	#35 - Nov 2002 Ferritin and Transferrin similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (2) #147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #224 - Aug 2018 Legumain similarity (1) #225 - Sep 2018 Phytase similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #58 - Oct 2004 G Proteins similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

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Related items in Molecule of the Month

#35 - Nov 2002
Ferritin and Transferrin
similarity (1)
#231 - Mar 2019
Measles Virus Proteins
similarity (2)
#147 - Mar 2012
Rhodopsin
similarity (1)
#100 - Apr 2008
Adrenergic Receptors
similarity (1)
#156 - Dec 2012
ABO Blood Type Glycosyltransferases
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (1)
#224 - Aug 2018
Legumain
similarity (1)
#225 - Sep 2018
Phytase
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#27 - Mar 2002
Bacteriorhodopsin
similarity (1)
#49 - Jan 2004
Carbonic Anhydrase
similarity (1)
#58 - Oct 2004
G Proteins
similarity (1)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: L-TRYPTOPHAN OXIDASE VIOA

B: L-TRYPTOPHAN OXIDASE VIOA

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	67.880, 87.070, 78.020
Angle α, β, γ (deg.)	90.00, 112.95, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (-0.99439, 0.10349, 0.02178), (0.10263, 0.99401, -0.03754), (-0.02554, -0.03509, -0.99906)
Vector: -79.39565, 6.52025, 112.57852)

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Protein , 1 types, 2 molecules AB

#1: Protein	L-TRYPTOPHAN OXIDASE VIOA Mass: 47245.676 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Strain: 12472 / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LAMBDA / References: UniProt: Q9S3V1, 7-chloro-L-tryptophan oxidase

#1: Protein

L-TRYPTOPHAN OXIDASE VIOA

Mass: 47245.676 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

CHROMOBACTERIUM VIOLACEUM (bacteria) / Strain: 12472 / Plasmid: PGEX / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LAMBDA / References: UniProt: Q9S3V1, 7-chloro-L-tryptophan oxidase

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Non-polymers , 7 types, 418 molecules

#2: Chemical	ChemComp-SM / SAMARIUM (III) ION Mass: 150.360 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Sm
#3: Chemical	ChemComp-HG / MERCURY (II) ION Mass: 200.590 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Hg
#4: Chemical	ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₅N₉O₁₅P₂
#5: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO₃
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.25 Å³/Da / Density % sol: 45.46 % / Description: NONE
Crystal grow	Temperature: 277 K / pH: 8.5 Details: 0.08 M TRIS PH 8.5, 24 %(W/V) PEG 4000, 0.16 M MGCL2, 20 %(V/V) GLYCEROL AT 277 K THEN SOAKED WITH 0.01 M HGCL2 AND 0.01 M SM(NO3)3

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.77001
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 22, 2013 / Details: TOROIDAL FOCUSING MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.77001 Å / Relative weight: 1
Reflection	Resolution: 2.08→19.92 Å / Num. obs: 49742 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 24.4 % / B_iso Wilson estimate: 23.7 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 26.34
Reflection shell	Resolution: 2.08→2.15 Å / Redundancy: 19.6 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 6.61 / % possible all: 91

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
SHELXCDE		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.076→19.984 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.23 / Stereochemistry target values: ML
Details: THE HYDROGEN ATOMS IN THE STRUCTURE ARE RIDING HYDROGENS AND THEIR POSITIONS WERE NOT REFINED

	R_factor	Num. reflection	% reflection
R_free	0.1881	4879	5 %
R_work	0.1648	-	-
obs	0.166	49741	98.39 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.74 Å²

Refinement step

Cycle: LAST / Resolution: 2.076→19.984 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6333	0	168	383	6884

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6669
X-RAY DIFFRACTION	f_angle_d	0.595	9044
X-RAY DIFFRACTION	f_dihedral_angle_d	13.81	3892
X-RAY DIFFRACTION	f_chiral_restr	0.041	948
X-RAY DIFFRACTION	f_plane_restr	0.003	1161

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 (%)
2.0761-2.0996	0.2501	130	0.2282	2445	X-RAY DIFFRACTION	80
2.0996-2.1243	0.2431	158	0.2026	3043	X-RAY DIFFRACTION	94
2.1243-2.1502	0.242	153	0.1986	2923	X-RAY DIFFRACTION	95
2.1502-2.1774	0.206	160	0.1873	3056	X-RAY DIFFRACTION	96
2.1774-2.206	0.2608	162	0.1882	3087	X-RAY DIFFRACTION	97
2.206-2.2362	0.2151	157	0.1802	3018	X-RAY DIFFRACTION	97
2.2362-2.2681	0.2159	161	0.1891	3062	X-RAY DIFFRACTION	98
2.2681-2.3019	0.2176	166	0.177	3126	X-RAY DIFFRACTION	98
2.3019-2.3378	0.198	161	0.177	3104	X-RAY DIFFRACTION	99
2.3378-2.3761	0.2122	164	0.1775	3071	X-RAY DIFFRACTION	99
2.3761-2.417	0.2036	167	0.1813	3145	X-RAY DIFFRACTION	100
2.417-2.4608	0.1942	165	0.1712	3096	X-RAY DIFFRACTION	100
2.4608-2.5081	0.2459	166	0.1613	3182	X-RAY DIFFRACTION	100
2.5081-2.5592	0.1931	165	0.1767	3120	X-RAY DIFFRACTION	100
2.5592-2.6147	0.1895	170	0.18	3166	X-RAY DIFFRACTION	100
2.6147-2.6754	0.2302	162	0.175	3104	X-RAY DIFFRACTION	100
2.6754-2.7421	0.2135	164	0.1735	3109	X-RAY DIFFRACTION	100
2.7421-2.8161	0.1811	167	0.1713	3199	X-RAY DIFFRACTION	100
2.8161-2.8987	0.2198	167	0.1774	3185	X-RAY DIFFRACTION	100
2.8987-2.992	0.1942	167	0.1738	3115	X-RAY DIFFRACTION	100
2.992-3.0985	0.2297	166	0.177	3142	X-RAY DIFFRACTION	100
3.0985-3.2221	0.1826	167	0.1734	3144	X-RAY DIFFRACTION	100
3.2221-3.3681	0.1556	161	0.1629	3136	X-RAY DIFFRACTION	100
3.3681-3.5447	0.1834	166	0.1586	3161	X-RAY DIFFRACTION	100
3.5447-3.7654	0.1533	168	0.1496	3137	X-RAY DIFFRACTION	100
3.7654-4.0539	0.1556	162	0.136	3125	X-RAY DIFFRACTION	100
4.0539-4.4578	0.1526	166	0.1328	3133	X-RAY DIFFRACTION	100
4.4578-5.0935	0.1587	165	0.1329	3155	X-RAY DIFFRACTION	100
5.0935-6.3824	0.1971	165	0.1655	3146	X-RAY DIFFRACTION	100
6.3824-19.9853	0.1543	161	0.1654	3143	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	1.1293	-0.0851	0.3085	0.9361	0.1979	1.2444	0.072	-0.0877	-0.1448	0.0726	0.0468	-0.0525	0.1553	0.0522	-0.1143	0.1626	0.03	-0.0063	0.1802	0.0177	0.1754	-26.5637	-3.4926	40.0201
2	1.3982	-0.3217	-0.4022	1.2341	-0.5198	1.2323	0.1537	0.0658	0.2649	0.0459	-0.0369	-0.09	-0.1632	0.0493	-0.1243	0.2179	0.0024	0.0078	0.1612	-0.0027	0.2517	-44.5077	9.4873	17.3668
3	1.2713	-0.2709	0.4274	0.4512	0.043	1.3143	0.0151	-0.095	-0.1281	-0.0197	0.0655	0.0125	0.0086	0.055	-0.0534	0.1705	0.0045	0.0042	0.1165	0.0414	0.1667	-33.2388	1.657	41.7432
4	1.5654	0.3576	0.2618	1.2061	0.4584	1.4237	-0.06	-0.5445	-0.4115	0.0297	0.1046	0.444	0.1229	-0.3557	-0.0121	0.1992	-0.0244	-0.0037	0.2897	0.1073	0.3642	-53.9753	-4.4788	38.802
5	0.7919	0.2532	-0.1811	1.1979	0.5761	1.109	-0.0374	0.0917	0.0979	-0.2812	0.1026	-0.0584	-0.3924	0.1513	-0.0404	0.2551	-0.0249	0.0075	0.1884	-0.0141	0.1859	-22.1833	10.8727	37.381
6	0.9904	0.0304	0.1513	0.8293	-0.0217	1.6682	0.1171	-0.1474	0.0027	0.141	0.0327	-0.058	0.0796	0.1643	-0.1593	0.1819	-0.0051	-0.0071	0.2335	-0.0335	0.1864	-7.026	-42.6964	73.9637
7	1.8538	-0.7855	0.5145	0.717	-0.3865	0.978	-0.0037	0.0807	0.15	-0.0373	0.0626	-0.0428	-0.0942	0.0583	-0.0584	0.2147	-0.0225	0.0032	0.2024	-0.0174	0.2323	-22.9045	-37.4656	50.8643
8	1.1198	0.098	0.5607	0.7497	0.2187	1.7609	0.0292	-0.0321	-0.0153	0.0228	0.1065	-0.0812	0.094	-0.1109	-0.1102	0.1814	0.0057	0.0054	0.2285	0.0026	0.2031	-11.6632	-47.3414	61.39
9	1.4348	-0.1277	0.1429	0.8035	-0.1422	0.7965	0.074	-0.4001	0.2366	0.1503	0.0429	-0.1201	-0.2277	0.1894	-0.0854	0.2722	-0.0699	-0.006	0.3793	-0.1225	0.2432	-6.0966	-31.6366	88.3846
10	1.6026	0.1828	0.4234	0.5363	0.4226	1.4045	-0.0128	-0.092	0.0372	-0.0532	-0.0178	0.1056	-0.0016	-0.1122	0.0242	0.1591	0.0072	0.0032	0.1489	0.0172	0.1614	-27.3822	-43.8627	66.7994
11	1.2871	0.1214	-0.3038	0.7332	-0.0191	0.8169	-0.0451	0.0139	0.1966	-0.1055	0.1397	-0.028	-0.1036	0.1384	-0.083	0.2158	-0.019	0.0014	0.2043	-0.0215	0.1669	-14.2365	-36.7541	68.1871

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 96 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 97 THROUGH 170 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 171 THROUGH 304 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 305 THROUGH 359 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 360 THROUGH 418 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 4 THROUGH 70 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 71 THROUGH 162 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 163 THROUGH 197 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 198 THROUGH 234 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 235 THROUGH 341 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 342 THROUGH 418 )

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