PDB-6ul2: Crystal structure of tryptophan-6-halogenase BorH complexed with ...

ID or keywords:

Entry

Database: PDB / ID: 6ul2

Title

Crystal structure of tryptophan-6-halogenase BorH complexed with L-tryptophan

Components

Tryptophan 6-halogenase

Keywords

FLAVOPROTEIN / halogenase oxidoreductase

Function / homology

Function and homology information

monooxygenase activity / nucleotide binding
Similarity search - Function

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.979 Å

Authors

Lingkon, K. / Bellizzi, J.J.

Citation

Journal: Chembiochem / Year: 2020
Title: Structure and Activity of the Thermophilic Tryptophan-6 Halogenase BorH.
Authors: Lingkon, K. / Bellizzi 3rd, J.J.

History

Deposition	Oct 6, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 6, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ul2.cif.gz	860.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6ul2.ent.gz	717.3 KB	Display	PDB format
PDBx/mmJSON format	6ul2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ul2_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6ul2_full_validation.pdf.gz	1.7 MB	Display
Data in XML	6ul2_validation.xml.gz	85.7 KB	Display
Data in CIF	6ul2_validation.cif.gz	122.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ul/6ul2 ftp://data.pdbj.org/pub/pdb/validation_reports/ul/6ul2	HTTPS FTP

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Related structure data

Related structure data	2oamS S: Starting model for refinement
Similar structure data	5icn-d 1fm6-1 1jvn-2 2vsm-d 6h44-1 6h43-2 4z43-d 1ktw-2 4h2c-d 6h44-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

2oamS

S: Starting model for refinement

Similar structure data

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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: Tryptophan 6-halogenase

B: Tryptophan 6-halogenase

C: Tryptophan 6-halogenase

D: Tryptophan 6-halogenase

hetero molecules

244 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tryptophan 6-halogenase

hetero molecules

defined by author
Evidence: gel filtration
61.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tryptophan 6-halogenase

hetero molecules

defined by author
61.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Tryptophan 6-halogenase

hetero molecules

defined by author
60.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Tryptophan 6-halogenase

hetero molecules

defined by author
61 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.480, 157.920, 113.250
Angle α, β, γ (deg.)	90.000, 104.060, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Tryptophan 6-halogenase Mass: 60202.082 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: borH / Production host: Escherichia coli (E. coli) / References: UniProt: M9QSI0
#2: Chemical	ChemComp-TRP / TRYPTOPHAN Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1276 / Source method: isolated from a natural source / Formula: H₂O
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: 2.65 Å³/Da / Density % sol: 53.53 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5 300 mM (NH4)2SO4 19% (w/v) PEG 8000.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 1.0332 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 8, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 1.979→32.06 Å / Num. obs: 170635 / % possible obs: 98.2 % / Redundancy: 4.8 % / CC_1/2: 0.983 / R_merge(I) obs: 0.162 / R_pim(I) all: 0.082 / R_rim(I) all: 0.182 / Net I/σ(I): 6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.98-2.01	4.9	0.798	41453	8445	0.677	0.399	0.895	2.2	99.2
10.84-32.06	4.7	0.114	4869	1030	0.979	0.058	0.129	10.3	94.5

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
Aimless	0.7.3	data scaling
MOSFLM		data reduction
PHASER		phasing
Coot		model building
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2OAM

2oam

Resolution: 1.979→31.8942 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.3 / Phase error: 22.82

	R_factor	Num. reflection	% reflection
R_free	0.2288	2000	1.17 %
R_work	0.1929	-	-
obs	0.1933	170571	98.16 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 118.77 Å² / B_iso mean: 35.3735 Å² / B_iso min: 5.05 Å²

Refinement step

Cycle: final / Resolution: 1.979→31.8942 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16681	0	195	1276	18152
B_iso mean	-	-	49.2	35.24	-
Num. residues	-	-	-	-	2081

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	17339
X-RAY DIFFRACTION	f_angle_d	0.881	23571
X-RAY DIFFRACTION	f_chiral_restr	0.037	2445
X-RAY DIFFRACTION	f_plane_restr	0.004	3083
X-RAY DIFFRACTION	f_dihedral_angle_d	12.173	6223

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.979-2.0285	0.2892	150	0.2575	12094	99
2.0285-2.0833	0.2832	143	0.2416	12114	99
2.0833-2.1446	0.2605	147	0.2206	12093	99
2.1446-2.2138	0.2432	137	0.2119	12143	99
2.2138-2.2929	0.2396	153	0.2001	12107	99
2.2929-2.3847	0.2799	139	0.2024	12086	99
2.3847-2.4932	0.2512	143	0.2061	12047	99
2.4932-2.6246	0.2819	136	0.2085	11723	95
2.6246-2.7889	0.2348	144	0.201	11635	95
2.7889-3.0041	0.2336	144	0.2004	12121	99
3.0041-3.3061	0.2274	146	0.1973	12190	99
3.3061-3.7839	0.2073	146	0.1794	12194	99
3.7839-4.7647	0.2096	134	0.1608	12069	98

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	3.1267	-0.8021	2.2598	0.8947	-0.5717	3.6278	-0.0044	0.1751	-0.011	-0.1181	0.1857	-0.2972	0.1676	0.3355	-0.1533	0.1772	-0.0075	0.0613	0.2347	-0.1071	0.2846	-10.6728	123.4308	125.7799
2	0.6832	-1.1521	0.0941	2.179	0.2182	1.2073	-0.1173	0.1742	0.0755	-0.14	0.0178	0.2123	-0.0931	-0.0506	0.0715	0.158	-0.0494	-0.0101	0.1673	0.0162	0.1914	-41.4535	130.2729	116.0723
3	1.5351	0.3454	0.5802	1.0531	0.3269	0.9578	-0.0663	0.0253	-0.2017	0.1052	0.1931	-0.1486	0.1236	0.1495	-0.0789	0.1814	0.0437	0.0386	0.1593	-0.0455	0.2413	-22.949	116.4712	131.0363
4	1.434	-0.7464	-0.2619	1.2201	0.7088	1.097	-0.0816	0.1117	0.2522	-0.1366	0.0351	-0.0603	-0.17	0.0164	0.0405	0.1958	-0.052	-0.0223	0.1362	0.038	0.2665	-37.5538	137.0537	122.1733
5	2.7068	0.0435	-1.6686	1.0218	0.2705	1.2335	-0.107	0.331	0.24	-0.2043	0.3559	0.8373	0.0059	-0.401	-0.1574	0.2095	-0.0233	-0.0516	0.3385	0.1896	0.6953	-8.0841	80.8961	125.1028
6	0.6634	-0.6154	0.1208	1.8277	-0.4201	1.2965	-0.0227	0.1435	0.0388	-0.2751	0.0047	0.0356	0.1857	0.0438	0.0106	0.1807	-0.0524	0.003	0.1778	-0.0044	0.1714	23.005	75.2105	115.5328
7	1.2759	1.0393	-0.5181	1.6787	-0.639	0.9608	0.0548	0.0476	0.4721	0.1399	0.1753	0.6464	-0.161	-0.167	-0.1175	0.1732	0.0328	0.0365	0.1825	0.0413	0.5212	4.5639	88.7905	130.7201
8	1.0929	-0.335	0.1656	1.309	-0.602	1.1325	-0.0818	0.089	-0.1798	-0.2194	0.1221	0.2315	0.2128	-0.0697	-0.0373	0.2	-0.0682	-0.0073	0.1456	-0.0035	0.2593	19.1229	68.4201	121.4434
9	4.0055	-1.1772	0.2017	3.4472	0.3951	1.7891	0.0427	-0.1127	-0.4903	0.0292	-0.0359	0.243	0.261	-0.1579	0.0297	0.2308	-0.0249	0.0309	0.1392	-0.0045	0.2728	-8.8977	122.4588	82.4377
10	2.1059	-0.5173	0.2169	2.0123	0.3512	1.5291	0.0741	0.0831	-0.3424	-0.1419	0.0304	-0.1111	0.1936	0.1704	-0.0877	0.273	0.1085	-0.0077	0.1922	-0.035	0.3398	18.304	120.6842	74.514
11	4.3333	0.9055	-0.4135	1.3979	0.0851	0.6794	0.1026	0.0292	-0.5032	0.1252	0.0035	-0.0276	0.2379	0.0692	-0.0916	0.2896	0.0733	-0.0247	0.2095	-0.0283	0.2836	16.7085	120.2683	80.6642
12	1.9984	-1.1025	-0.3821	1.2331	0.2468	1.0272	0.2396	0.3898	-0.4801	-0.1672	-0.2327	0.305	0.2137	-0.1718	0.0264	0.2947	0.0406	-0.0467	0.2626	-0.1137	0.3237	-10.1288	123.0094	68.7142
13	1.6839	0.5872	0.3833	1.0364	0.2785	2.1927	0.5388	0.3493	-1.3137	-0.6413	-0.3548	-0.0512	0.497	-0.2883	0.2035	0.5867	0.366	-0.0129	0.3232	-0.4176	0.173	11.2736	116.2005	58.8386
14	2.1123	-0.9381	-0.6077	1.2664	0.4296	1.5553	0.1967	0.3925	-0.1293	-0.2164	-0.1683	0.0092	0.1053	0.0966	-0.0069	0.2261	0.0676	0.0002	0.2385	-0.0495	0.227	1.6762	130.6798	68.0608
15	2.2019	0.0912	-0.12	2.2139	0.0561	0.8511	0.0524	-0.0806	-0.0261	0.1766	0.0168	-0.2682	0.1205	0.115	-0.0671	0.244	0.0669	0.0353	0.2236	-0.0525	0.3282	21.9983	131.6568	80.2406
16	2.2914	-0.0685	-0.2222	2.3634	-0.4947	0.9408	-0.1621	-0.1885	0.5572	0.0499	0.0678	-0.1408	-0.2643	0.0566	0.06	0.2842	-0.0451	-0.0906	0.1883	0.0067	0.6107	-8.6782	82.411	81.7357
17	0.7416	0.2123	-0.4315	1.6959	-0.2582	0.898	-0.1616	-0.0404	1.1573	0.0114	0.0942	0.4331	-0.2627	-0.2995	0.0119	0.3374	0.0303	-0.1676	0.1773	0.1874	0.8852	-36.2206	84.475	73.1076
18	1.635	1.3014	0.3356	1.1356	0.4307	0.4931	-0.1141	-0.2753	0.6306	-0.0636	-0.0094	0.111	-0.2527	-0.1519	0.0689	0.3094	0.0128	-0.1019	0.2479	0.0967	0.8239	-35.2076	84.6954	79.2371
19	0.3514	-0.1315	0.3474	0.9827	-0.2893	0.7807	-0.1609	0.4943	0.8653	-0.1892	0.001	-0.0575	-0.2323	0.2448	0.0785	0.3294	-0.0923	-0.1043	0.3316	0.2002	0.7286	-7.9062	81.7302	67.5658
20	1.5999	-0.4132	0.0634	0.8891	-0.1353	0.6776	-0.0072	0.5382	0.6352	-0.2733	0.0277	0.0958	-0.1543	0.1819	0.1063	0.3241	-0.0926	-0.1034	0.2586	0.2689	0.6004	-20.4541	79.2866	65.6396
21	1.5657	0.5201	0.1069	1.9393	-0.4947	0.8482	-0.0744	0.0113	0.5016	0.0443	0.1004	0.2453	-0.1147	-0.1247	-0.0395	0.2394	0.0072	-0.1027	0.223	0.0772	0.5055	-39.1645	73.3131	75.2544

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 80 )	A	2 - 80
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 81 through 161 )	A	81 - 161
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 162 through 427 )	A	162 - 427
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 428 through 527 )	A	428 - 527
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 80 )	B	2 - 80
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 81 through 161 )	B	81 - 161
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 162 through 427 )	B	162 - 427
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 428 through 527 )	B	428 - 527
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 3 through 63 )	C	3 - 63
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 64 through 121 )	C	64 - 121
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 122 through 187 )	C	122 - 187
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 188 through 272 )	C	188 - 272
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 273 through 315 )	C	273 - 315
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 316 through 427 )	C	316 - 427
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 428 through 527 )	C	428 - 527
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 3 through 63 )	D	3 - 63
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 64 through 121 )	D	64 - 121
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 122 through 187 )	D	122 - 187
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 188 through 272 )	D	188 - 272
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 273 through 409 )	D	273 - 409
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 410 through 527 )	D	410 - 527

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