PDB-8ttj: Tryptophan-6-halogenase BorH complexed with 6-chlorotryptophan

ID or keywords:

Entry

Database: PDB / ID: 8ttj

Title

Tryptophan-6-halogenase BorH complexed with 6-chlorotryptophan

Components

Tryptophan 6-halogenase

Keywords

FLAVOPROTEIN / halogenase oxidoreductase

Function / homology

Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / nucleotide binding / 6-CHLORO-L-TRYPTOPHAN / Tryptophan 6-halogenase

Function and homology information

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.98 Å

Authors

Lingkon, K. / Bellizzi, J.J.

Funding support

United States, 1items

Citation

Journal: Biorxiv / Year: 2023
Title: Crystallographic and thermodynamic evidence of negative cooperativity of flavin and tryptophan binding in the flavin-dependent halogenases AbeH and BorH.
Authors: Ashaduzzaman, M. / Lingkon, K. / De Silva, A.J. / Bellizzi, J.J.

History

Deposition	Aug 14, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 30, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8ttj.cif.gz	871.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8ttj.ent.gz	725 KB	Display	PDB format
PDBx/mmJSON format	8ttj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8ttj_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8ttj_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8ttj_validation.xml.gz	88.6 KB	Display
Data in CIF	8ttj_validation.cif.gz	126.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tt/8ttj ftp://data.pdbj.org/pub/pdb/validation_reports/tt/8ttj	HTTPS FTP

-
Related structure data

Related structure data	8fovC 8foxC 8ttiC 8ttkC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

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

3

C: Tryptophan 6-halogenase

hetero molecules

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

4

D: Tryptophan 6-halogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.520, 157.971, 112.580
Angle α, β, γ (deg.)	90.00, 104.06, 90.00
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-6CW / 6-CHLORO-L-TRYPTOPHAN Type: L-peptide linking / Mass: 238.670 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₁ClN₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1426 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.29 %
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.

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 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: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.98→35.47 Å / Num. obs: 169702 / % possible obs: 98.24 % / Redundancy: 2 % / B_iso Wilson estimate: 27.43 Å² / CC_1/2: 0.987 / CC star: 0.997 / R_merge(I) obs: 0.09909 / R_pim(I) all: 0.09909 / R_rim(I) all: 0.1401 / Net I/σ(I): 4.91
Reflection shell	Resolution: 1.98→2.051 Å / Redundancy: 2 % / R_merge(I) obs: 0.7698 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 16993 / CC_1/2: 0.247 / CC star: 0.629 / R_pim(I) all: 0.7698 / % possible all: 28.67

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.98→35.47 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2365	1997	1.18 %	random
R_work	0.1993	-	-	-
obs	0.1997	169702	98.27 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 37.53 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→35.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16755	0	204	1426	18385

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	17429
X-RAY DIFFRACTION	f_angle_d	0.532	23689
X-RAY DIFFRACTION	f_dihedral_angle_d	5.437	2322
X-RAY DIFFRACTION	f_chiral_restr	0.041	2450
X-RAY DIFFRACTION	f_plane_restr	0.005	3100

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 (%)
1.98-2.03	0.4106	141	0.3362	11947	X-RAY DIFFRACTION	99
2.03-2.08	0.3395	135	0.311	12021	X-RAY DIFFRACTION	99
2.08-2.14	0.3003	155	0.2848	11968	X-RAY DIFFRACTION	99
2.14-2.21	0.3429	127	0.2648	12057	X-RAY DIFFRACTION	99
2.21-2.29	0.2894	139	0.2391	12056	X-RAY DIFFRACTION	99
2.29-2.38	0.2575	159	0.2244	12046	X-RAY DIFFRACTION	99
2.38-2.49	0.2546	141	0.2178	12032	X-RAY DIFFRACTION	99
2.49-2.62	0.2787	144	0.2131	11658	X-RAY DIFFRACTION	96
2.62-2.79	0.2479	133	0.1998	11827	X-RAY DIFFRACTION	97
2.79-3	0.2144	146	0.1954	12151	X-RAY DIFFRACTION	99
3-3.31	0.2259	145	0.1876	12129	X-RAY DIFFRACTION	99
3.31-3.78	0.1995	150	0.1703	12027	X-RAY DIFFRACTION	98
3.78-4.77	0.1893	136	0.1505	11968	X-RAY DIFFRACTION	98
4.77-35.47	0.204	146	0.177	11999	X-RAY DIFFRACTION	97

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	3.4505	-0.4737	1.6618	1.9603	-0.0747	3.3688	-0.0117	0.3115	-0.0171	-0.112	0.1776	-0.3866	0.0186	0.5018	-0.162	0.1826	-0.0147	0.0532	0.2307	-0.0779	0.2381	-9.4229	124.3225	125.8915
2	1.2699	-1.3988	-0.1483	2.3293	0.0542	1.0154	-0.06	0.2674	0.1228	-0.2207	-0.0003	0.2203	-0.0774	0.0319	0.0446	0.1851	-0.0376	-0.0325	0.2001	0.0196	0.1313	-40.6958	130.1222	115.5843
3	2.2493	-0.2912	0.9724	1.3121	-0.3812	3.2304	0.0389	0.1254	-0.2155	0.0158	0.1544	-0.245	0.4624	0.6508	-0.1716	0.2386	0.0644	-0.0159	0.2783	-0.1132	0.2784	-8.4459	116.7455	132.9506
4	2.6397	0.5547	0.7651	2.5838	0.3472	0.2354	-0.0656	0.2022	-0.2041	-0.1995	0.1189	-0.228	0.1973	-0.0068	-0.0401	0.1852	-0.0245	0.0454	0.1456	-0.0537	0.1679	-33.0801	110.5546	121.2493
5	2.4672	1.0619	1.1485	0.9931	0.3489	0.9178	-0.0493	-0.012	-0.0944	0.1047	0.1018	-0.0479	0.1047	0.0942	-0.0574	0.1879	0.0328	0.0296	0.1601	-0.0282	0.1308	-26.8576	120.0201	134.6646
6	2.1497	-0.7004	-0.4038	1.5761	0.6482	1.3334	-0.0878	0.2357	0.3725	-0.1868	0.0347	-0.0194	-0.1718	0.066	0.0462	0.1914	-0.0601	-0.0315	0.1595	0.0514	0.1984	-37.5433	137.0506	121.8891
7	3.2376	0.0393	-1.9235	1.5504	0.1358	2.6135	-0.0644	0.2582	0.16	-0.1482	0.1309	0.8622	-0.0539	-0.4861	-0.0697	0.2244	-0.0135	-0.0601	0.3214	0.1087	0.5662	-7.924	80.9773	124.1692
8	0.6588	-1.2744	0.2912	4.813	0.0734	1.1865	-0.0381	0.1586	0.0265	-0.4168	-0.0171	-0.1302	0.1209	0.1403	0.0662	0.1916	-0.0335	0.0085	0.1941	-0.0006	0.1169	25.3852	75.4757	116.142
9	2.3783	0.0986	-1.277	0.7372	-0.3541	2.1432	0.208	0.0692	0.5135	0.0881	0.1425	0.5903	-0.3709	-0.509	-0.3392	0.2901	0.0207	0.0837	0.3144	0.0833	0.6924	-7.8899	87.0252	129.2925
10	2.3766	0.4948	0.0913	3.9278	0.0161	0.1275	-0.0816	0.0593	0.381	-0.2635	0.077	0.3647	-0.5939	0.1867	0.0038	0.1343	-0.0343	0.0311	0.1747	0.0281	0.3969	12.5332	92.4468	121.546
11	1.6579	1.3084	-0.7789	1.9121	-0.7315	1.3116	0.0608	-0.0055	0.3557	0.1458	0.0893	0.4768	-0.1578	-0.1078	-0.159	0.1745	0.0084	0.0135	0.147	-0.0197	0.3038	10.8593	88.2435	130.1035
12	1.6443	-0.4177	0.675	1.8351	-0.574	1.607	-0.0285	0.1255	-0.1249	-0.2216	0.039	0.2731	0.2092	-0.111	-0.0122	0.1841	-0.0486	0.0009	0.1503	-0.0111	0.2114	19.2478	68.5149	120.3355
13	6.3328	-1.0917	-0.0811	1.6868	-0.2206	2.0649	0.0834	-0.1655	-0.6285	-0.0469	-0.0392	0.2052	0.3739	-0.0087	-0.0511	0.258	-0.0248	0.0008	0.1299	-0.0063	0.2425	-5.6483	119.5909	82.6056
14	1.5424	0.8161	1.065	1.814	1.1745	3.4309	0.0852	0.3627	-0.0742	-0.1188	0.2214	-0.5681	0.427	0.7162	-0.2997	0.3151	0.1753	0.0356	0.3483	-0.034	0.3299	24.3704	124.3773	69.8099
15	3.1375	-0.6666	-0.1121	0.7949	-0.0307	0.5389	0.1416	0.202	-0.5349	-0.0332	-0.0936	0.162	0.1963	-0.037	-0.0513	0.2895	0.0257	-0.0101	0.2198	-0.0822	0.2313	-0.3141	123.07	75.6739
16	1.3631	0.7815	-0.3904	0.9574	-0.4065	3.592	0.2061	0.4476	-0.3603	-0.5644	-0.1445	-0.2121	0.6108	0.0421	-0.0496	0.4291	0.1615	-0.0174	0.4222	-0.1584	0.3391	11.2483	115.8234	61.0102
17	2.7496	-0.9502	-1.2048	1.1013	0.4641	2.0426	0.2143	0.4444	-0.2171	-0.2726	-0.2233	0.0333	0.0855	0.0578	0.0043	0.2261	0.0642	-0.0166	0.2531	-0.0416	0.1751	1.7476	130.3314	67.7634
18	2.3741	0.3724	-0.0917	2.4623	0.2842	1.1031	0.0804	-0.0797	-0.0024	0.256	0.0426	-0.2264	0.1576	0.146	-0.1096	0.2314	0.0762	-0.0013	0.2391	-0.0419	0.2082	22.056	131.5109	80.0815
19	3.7041	-0.9707	0.2341	1.5362	0.2172	1.3099	-0.1728	0.0792	0.5555	-0.0621	0.0954	0.01	-0.3073	0.0961	0.0781	0.2909	-0.0502	-0.0893	0.1927	0.0519	0.6157	-8.4196	82.8737	79.7567
20	0.886	0.4267	-1.069	1.8699	-0.2146	1.8976	-0.1995	0.1649	0.7214	-0.1603	0.1807	0.0476	-0.2889	-0.3208	0.0308	0.3113	0.0305	-0.1173	0.2834	0.1406	0.7704	-35.7921	84.3287	71.9084
21	1.7186	1.7108	-0.5574	5.2462	0.4607	1.0415	-0.1593	-0.0639	0.8455	-0.0163	0.0615	0.5252	-0.2751	-0.1999	0.0928	0.246	0.0461	-0.0624	0.2851	0.0612	0.5983	-45.5337	80.2737	77.0148
22	2.8067	-0.0926	-0.0539	1.8559	-0.0378	1.0774	-0.067	0.227	0.943	-0.1146	0.0379	-0.3368	-0.3315	0.2084	0.018	0.3124	-0.0835	-0.0895	0.3166	0.1406	0.6029	-4.3742	82.5751	72.0434
23	1.3557	-0.0293	0.464	2.0532	-0.9243	2.1343	-0.0352	0.5038	0.8121	-0.4421	0.0032	-0.0479	-0.5576	0.0468	0.0384	0.4603	-0.0783	-0.1828	0.4682	0.3148	0.7566	-28.6201	88.851	58.5761
24	1.5927	-0.647	0.4802	0.7265	-0.1517	1.014	-0.1331	0.4825	0.6711	-0.2304	0.0139	-0.0302	-0.1751	0.0078	0.1214	0.2784	-0.0811	-0.081	0.3283	0.1858	0.4333	-18.9085	73.9937	65.8846
25	1.7326	0.8761	0.1238	2.168	-0.4578	0.9983	-0.0566	-0.0202	0.6272	0.1463	0.0437	0.4422	-0.1824	-0.1745	0.0063	0.2118	0.0371	-0.056	0.2781	0.0668	0.4751	-39.4869	73.3902	78.0117

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 76 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 77 through 161 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 162 through 242 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 243 through 315 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 316 through 427 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 428 through 527 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 80 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 81 through 151 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 152 through 242 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 243 through 271 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 272 through 427 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 428 through 528 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 2 through 80 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 81 through 121 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 122 through 245 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 246 through 315 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 316 through 427 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 428 through 527 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 3 through 63 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 64 through 121 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 122 through 161 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 162 through 245 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 246 through 316 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 317 through 427 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 428 through 527 )

-
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://pdbjlvh1.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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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