PDB-8rs4: Flavin-dependent tryptophan 6-halogenase Thal in complex with try...

ID or keywords:

Entry

Database: PDB / ID: 8rs4

Title

Flavin-dependent tryptophan 6-halogenase Thal in complex with tryptoline

Components

Tryptophan 6-halogenase ThaL

Keywords

FLAVOPROTEIN / flavin-dependent / halogenase / non-native substrate / unnatural substrate / tryptoline

Function / homology

Function and homology information

tryptophan 6-halogenase / monooxygenase activity / nucleotide binding
Similarity search - Function

Biological species

Streptomyces albogriseolus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.2 Å

Authors

Bork, S. / Niemann, H.H.

Funding support

Germany, 1items

Citation

Journal: Chembiochem / Year: 2025
Title: Structural Basis of Regioselective Bromination of Tricyclic Tryptoline by the Tryptophan Halogenase Thal.
Authors: Bork, S. / Besse, C. / Sewald, N. / Niemann, H.H.

History

Deposition	Jan 24, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 4, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8rs4.cif.gz	543 KB	Display	PDBx/mmCIF format
PDB format	pdb8rs4.ent.gz	371.9 KB	Display	PDB format
PDBx/mmJSON format	8rs4.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/rs/8rs4 ftp://data.pdbj.org/pub/pdb/validation_reports/rs/8rs4	HTTPS FTP

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Related structure data

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: Tryptophan 6-halogenase ThaL

B: Tryptophan 6-halogenase ThaL

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, homodimer in crystal monomer in solution

Unit cell

Length a, b, c (Å)	137.590, 137.590, 144.050
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	172
Space group name H-M	P6₄
Space group name Hall	P6₄
Symmetry operation	#1: x,y,z #2: x-y,x,z+2/3 #3: y,-x+y,z+1/3 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: -x,-y,z

Components on special symmetry positions

ID	Model	Components
1	1	A-1022- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 2 through 53 or resid 55...
d_2	ens_1	(chain "B" and (resid 2 through 53 or resid 55...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	ASP	ASP	PRO	PRO	A	A	2 - 53	4 - 55
d_1	2	LEU	LEU	MET	MET	A	A	55 - 71	57 - 73
d_1	3	GLU	GLU	GLU	GLU	A	A	73	75
d_1	4	ALA	ALA	LYS	LYS	A	A	76 - 79	78 - 81
d_1	5	ALA	ALA	ALA	ALA	A	A	81 - 146	83 - 148
d_1	6	THR	THR	LEU	LEU	A	A	148 - 181	150 - 183
d_1	7	ASN	ASN	LYS	LYS	A	A	183 - 188	185 - 190
d_1	8	ALA	ALA	VAL	VAL	A	A	190 - 194	192 - 196
d_1	9	ASP	ASP	GLU	GLU	A	A	196 - 197	198 - 199
d_1	10	THR	THR	LEU	LEU	A	A	199 - 212	201 - 214
d_1	11	THR	THR	GLN	GLN	A	A	214 - 306	216 - 308
d_1	12	GLU	GLU	ASN	ASN	A	A	308 - 327	310 - 329
d_1	13	VAL	VAL	VAL	VAL	A	A	329	331
d_1	14	PHE	PHE	ILE	ILE	A	A	331 - 365	333 - 367
d_1	15	ALA	ALA	ALA	ALA	A	A	367 - 368	369 - 370
d_1	16	HIS	HIS	ALA	ALA	A	A	370 - 373	372 - 375
d_1	17	HIS	HIS	ASP	ASP	A	A	375 - 450	377 - 452
d_1	18	ASN	ASN	PRO	PRO	A	A	464 - 482	466 - 484
d_1	19	ASN	ASN	ALA	ALA	A	A	484 - 497	486 - 499
d_1	20	ALA	ALA	LYS	LYS	A	A	499 - 507	501 - 509
d_1	21	LYS	LYS	VAL	VAL	A	A	509 - 514	511 - 516
d_1	22	SER	SER	LEU	LEU	A	A	516 - 524	518 - 526
d_1	23	GLN	GLN	HIS	HIS	A	A	526 - 528	528 - 530
d_2	1	ASP	ASP	PRO	PRO	B	B	2 - 53	4 - 55
d_2	2	LEU	LEU	MET	MET	B	B	55 - 71	57 - 73
d_2	3	GLU	GLU	GLU	GLU	B	B	73	75
d_2	4	ALA	ALA	LYS	LYS	B	B	76 - 79	78 - 81
d_2	5	ALA	ALA	ALA	ALA	B	B	81 - 146	83 - 148
d_2	6	THR	THR	LEU	LEU	B	B	148 - 181	150 - 183
d_2	7	ASN	ASN	LYS	LYS	B	B	183 - 188	185 - 190
d_2	8	ALA	ALA	VAL	VAL	B	B	190 - 194	192 - 196
d_2	9	ASP	ASP	GLU	GLU	B	B	196 - 197	198 - 199
d_2	10	THR	THR	LEU	LEU	B	B	199 - 212	201 - 214
d_2	11	THR	THR	GLN	GLN	B	B	214 - 306	216 - 308
d_2	12	GLU	GLU	ASN	ASN	B	B	308 - 327	310 - 329
d_2	13	VAL	VAL	VAL	VAL	B	B	329	331
d_2	14	PHE	PHE	ILE	ILE	B	B	331 - 365	333 - 367
d_2	15	ALA	ALA	ALA	ALA	B	B	367 - 368	369 - 370
d_2	16	HIS	HIS	ALA	ALA	B	B	370 - 373	372 - 375
d_2	17	HIS	HIS	ASP	ASP	B	B	375 - 450	377 - 452
d_2	18	ASN	ASN	PRO	PRO	B	B	464 - 482	466 - 484
d_2	19	ASN	ASN	ALA	ALA	B	B	484 - 497	486 - 499
d_2	20	ALA	ALA	LYS	LYS	B	B	499 - 507	501 - 509
d_2	21	LYS	LYS	VAL	VAL	B	B	509 - 514	511 - 516
d_2	22	SER	SER	LEU	LEU	B	B	516 - 524	518 - 526
d_2	23	GLN	GLN	HIS	HIS	B	B	526 - 528	528 - 530

NCS oper: (Code: givenMatrix: (-0.991285623964, -0.0609781520692, -0.116766761937), (-0.0646201833959, -0.547330773775, 0.834417914463), (-0.114791304639, 0.834691972556, 0.538620708226)Vector: 116. ...

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Protein , 1 types, 2 molecules AB

#1: Protein	Tryptophan 6-halogenase ThaL / Trp 6-halogenase / FADH(2)-dependent tryptophan 6-halogenase Mass: 60219.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thaL, thdH / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280, tryptophan 6-halogenase

#1: Protein

Tryptophan 6-halogenase ThaL / Trp 6-halogenase / FADH(2)-dependent tryptophan 6-halogenase

Mass: 60219.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptomyces albogriseolus (bacteria) / Gene: thaL, thdH / Plasmid: pETM-11 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280, tryptophan 6-halogenase

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Non-polymers , 5 types, 576 molecules

#2: Chemical	ChemComp-WYH / 2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole Mass: 172.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.7 % / Description: hexagonal prism
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: reservoir: 0.1 M bicine pH 8.0, 1.6 M KH2PO4/K2HPO4; protein: 15 mg/mL Thal-wt (10 mM Tris pH 7.4, 50 mM NaCl, 1 mM DTT); Ratio: 100 nL protein + 100 nL reservoir

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 19, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 78305 / % possible obs: 100 % / Redundancy: 10.46 % / B_iso Wilson estimate: 42.8 Å² / CC_1/2: 0.998 / R_rim(I) all: 0.157 / Net I/σ(I): 15.35
Reflection shell	Resolution: 2.2→2.26 Å / Redundancy: 9.48 % / Mean I/σ(I) obs: 0.99 / Num. unique obs: 5792 / CC_1/2: 0.353 / R_rim(I) all: 2.56 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS	BUILT=20220820	data reduction
XSCALE	BUILT=20220820	data scaling
Coot	0.9.8.1	model building
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 2.2→45.04 Å / SU ML: 0.2849 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2037	3913	5 %
R_work	0.1688	74329	-
obs	0.1705	78242	99.91 %

Solvent computation

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

Displacement parameters

B_iso mean: 53.71 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→45.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8331	0	121	558	9010

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0081	8902
X-RAY DIFFRACTION	f_angle_d	1.136	12107
X-RAY DIFFRACTION	f_chiral_restr	0.0738	1264
X-RAY DIFFRACTION	f_plane_restr	0.0119	1580
X-RAY DIFFRACTION	f_dihedral_angle_d	14.5627	3252

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.5034097947 Å

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 (%)
2.2-2.23	0.2943	140	0.289	2658	X-RAY DIFFRACTION	100
2.23-2.26	0.2762	140	0.2834	2651	X-RAY DIFFRACTION	100
2.26-2.28	0.3359	139	0.262	2652	X-RAY DIFFRACTION	100
2.28-2.32	0.299	140	0.2685	2658	X-RAY DIFFRACTION	100
2.32-2.35	0.311	139	0.2672	2633	X-RAY DIFFRACTION	100
2.35-2.38	0.3038	139	0.2573	2650	X-RAY DIFFRACTION	99.96
2.38-2.42	0.3075	139	0.2454	2641	X-RAY DIFFRACTION	99.93
2.42-2.46	0.2843	140	0.2381	2662	X-RAY DIFFRACTION	100
2.46-2.5	0.306	139	0.2338	2634	X-RAY DIFFRACTION	100
2.5-2.55	0.2436	140	0.2229	2660	X-RAY DIFFRACTION	100
2.55-2.6	0.2775	139	0.2243	2650	X-RAY DIFFRACTION	100
2.6-2.65	0.2595	140	0.2139	2653	X-RAY DIFFRACTION	100
2.65-2.71	0.2734	139	0.2057	2630	X-RAY DIFFRACTION	100
2.71-2.77	0.2401	140	0.1922	2659	X-RAY DIFFRACTION	100
2.77-2.84	0.2645	139	0.1897	2644	X-RAY DIFFRACTION	100
2.84-2.92	0.2229	139	0.1879	2644	X-RAY DIFFRACTION	100
2.92-3	0.2259	141	0.19	2674	X-RAY DIFFRACTION	100
3-3.1	0.2308	139	0.1939	2645	X-RAY DIFFRACTION	100
3.1-3.21	0.2434	140	0.1942	2673	X-RAY DIFFRACTION	100
3.21-3.34	0.257	140	0.1851	2649	X-RAY DIFFRACTION	100
3.34-3.49	0.2209	139	0.1665	2653	X-RAY DIFFRACTION	99.96
3.49-3.68	0.1897	140	0.1555	2659	X-RAY DIFFRACTION	100
3.68-3.91	0.1725	141	0.1486	2673	X-RAY DIFFRACTION	100
3.91-4.21	0.1595	139	0.1215	2644	X-RAY DIFFRACTION	100
4.21-4.63	0.1283	141	0.1076	2673	X-RAY DIFFRACTION	100
4.63-5.3	0.1078	141	0.1105	2674	X-RAY DIFFRACTION	100
5.3-6.67	0.1844	140	0.1502	2668	X-RAY DIFFRACTION	100
6.67-45.04	0.1722	141	0.1483	2665	X-RAY DIFFRACTION	97.74

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	4.02411375607	-1.18590279656	-4.28281502036	1.15576027402	1.92917588496	5.55716637247	-0.0503892399269	-0.437393100212	-0.134815094257	0.131374720083	0.114830102752	-0.0373695066417	-0.0785062557287	0.544731826366	0.030964935461	0.28031009665	-0.0577446085282	-0.000517292543956	0.397997175065	0.010154710655	0.271248169838	17.6523883327	-44.6984657095	-23.9200197748
2	0.865145428384	0.197764701964	-0.378806860554	0.425624972523	-0.132216347064	1.01220962011	-0.0101160782316	-0.0426236790072	0.0975305907466	0.0171395764219	0.0277462074052	0.0127375712027	-0.133388518275	0.0322282524564	-0.0226629557133	0.33515290744	-0.00523919494064	0.0368735429983	0.300066949477	0.00907725629936	0.289282485392	1.6412343088	-40.6045468778	-25.6410757367
3	2.13342994683	1.53836049113	0.692083378357	1.50033419169	0.646752326829	1.6569397769	-0.035700507434	0.0212464605303	-0.166727622502	0.0126151664289	0.0364194727634	-0.204066553455	0.0378587225094	0.27023943102	-0.0292524281193	0.401878479361	0.066777173965	0.0423301395364	0.391277191815	0.0183406169537	0.343321017839	-7.82114303107	-53.6771408006	-13.0681647432
4	5.74594082139	-1.55711289418	-1.87973728832	2.44722246541	-0.242177971377	2.08435417979	-0.288850072025	-0.375245613259	-0.627952290953	-0.140718662081	-0.0484878393964	-0.294225949047	0.109946852682	0.325675157557	0.228933411886	0.321484481477	-0.00429640135359	0.0972571534043	0.372429785421	0.103945659473	0.424051384881	-15.4801138253	-85.3568471756	-16.0197024292
5	2.73934770143	2.25875481781	-0.420638307266	3.21512252929	0.0543686901043	0.77665806182	-0.418622142006	-0.276631113896	-1.04657455813	-0.0242893540846	0.11376536618	-0.464878988078	0.257215849651	0.245689185209	0.253725491449	0.51758254265	0.0945581886475	0.268282550447	0.528799689992	0.126359897394	0.806569573456	14.5646463301	-84.0009735737	-32.6870918082
6	3.90017782978	-0.0206465541845	0.0297099365364	1.30477623916	-1.18809908118	2.32814725351	-0.164591026757	0.0158673576226	-0.723184445539	-0.193451895665	0.0250356205651	-0.133155887004	0.241277814209	-0.0301614969069	0.108754539999	0.382239542573	-0.0298845459802	0.0941837783832	0.282647694761	0.00739170230132	0.456677061804	-21.1162473719	-86.3979749004	-20.6979942206
7	2.39364281544	0.750804653415	-0.923532986003	0.904463566512	-0.231933996746	1.88643096695	-0.526822256233	0.423788544743	-1.06517558001	-0.355578633446	0.00866927220191	-0.303404876968	0.527618203514	-0.0711098947544	0.170386265117	0.561107244937	-0.0819712683404	0.277411190214	0.381234562548	-0.0999527532797	0.665246611566	-8.7994450046	-87.2929723413	-34.3620748746
8	5.98435998509	0.708710285527	0.789650743309	4.14872923261	0.432502227965	0.14274325237	-0.181654965547	-0.182108513078	-0.153682229201	0.0289041498084	-0.0225789348582	0.188970066422	0.141035833858	-0.0425320230436	0.167475940873	0.455925851494	-0.0228192245245	0.146011723921	0.378738143804	0.00683309590796	0.367006895056	8.6613350987	-71.0498638008	-35.6671285495
9	0.987111077072	1.53326391412	-0.863077640479	4.6724211433	-3.30519533847	2.46813803113	-0.116536149424	-1.1249880242	-0.950216737288	0.286416028357	-0.455457313494	-0.220177072325	0.128909196119	0.418251120456	0.572625047011	0.51757176811	0.124375812096	0.156241540199	0.806580058673	0.391948664699	0.84421672718	17.3324152161	-84.6376615885	-17.2621184749

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 'A' and (resid 2 through 80 )	A	A	2 - 80	1 - 79
2	2	chain 'A' and (resid 81 through 428 )	A	A	81 - 428	80 - 427
3	3	chain 'A' and (resid 429 through 529 )	A	A	429 - 529	428 - 528
4	4	chain 'B' and (resid 2 through 80 )	B	J	2 - 80	1 - 79
5	5	chain 'B' and (resid 81 through 152 )	B	J	81 - 152	80 - 151
6	6	chain 'B' and (resid 153 through 243 )	B	J	153 - 243	152 - 242
7	7	chain 'B' and (resid 244 through 428 )	B	J	244 - 428	243 - 427
8	8	chain 'B' and (resid 429 through 492 )	B	J	429 - 492	428 - 479
9	9	chain 'B' and (resid 493 through 529 )	B	J	493 - 529	480 - 516

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 576 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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+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 , 5 types, 576 molecules

-
Details

-
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