PDB-2wet: Crystal structure of tryptophan 5-halogenase (PyrH) complex with ...

ID or keywords:

Entry

Database: PDB / ID: 2wet

Title

Crystal structure of tryptophan 5-halogenase (PyrH) complex with FAD (tryptophan)

Components

TRYPTOPHAN 5-HALOGENASE

Keywords

ANTIFUNGAL PROTEIN /

REGIOSELECTIVITY / TRYPTOPHAN 5-HALOGENASE

Function / homology

Function and homology information

tryptophan 5-halogenase / antibiotic biosynthetic process /

monooxygenase activity /

nucleotide binding
Similarity search - Function

Biological species

STREPTOMYCES RUGOSPORUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

De Laurentis, W. / Zhu, X. / Naismith, J.H.

Citation

Journal: J.Mol.Biol. / Year: 2009
Title: Structural Insights in the Regioselectivity in the Enzymatic Chlorination of Tryptophan.
Authors: Zhu, X. / De Laurentis, W. / Leang, K. / Herrmann, J. / Ihlefeld, K. / Van Pee, K.H. / Naismith, J.H.

History

Deposition	Apr 1, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 14, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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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PDBx/mmCIF format	2wet.cif.gz	416.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/we/2wet ftp://data.pdbj.org/pub/pdb/validation_reports/we/2wet	HTTPS FTP

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Related structure data

Related structure data	2wesC 2weuC 2aqjS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2wes-2 6nsd-d 2weu-2 2wes-1 2weu-1 6y1w-d 5hy5-d 2wcg-d 6sls-d 5lv9-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

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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 5-HALOGENASE

B: TRYPTOPHAN 5-HALOGENASE

C: TRYPTOPHAN 5-HALOGENASE

D: TRYPTOPHAN 5-HALOGENASE

hetero molecules

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

1

A: TRYPTOPHAN 5-HALOGENASE

D: TRYPTOPHAN 5-HALOGENASE

hetero molecules

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

2

B: TRYPTOPHAN 5-HALOGENASE

C: TRYPTOPHAN 5-HALOGENASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	137.530, 137.530, 307.830
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
3	1	D
1	2	A
2	2	B
1	3	A
2	3	B
3	3	C
4	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ILE	ILE	GLU	GLU	1	A	A	2 - 375	2 - 375
2	1	1	ILE	ILE	GLU	GLU	1	C	C	2 - 375	2 - 375
3	1	1	ILE	ILE	GLU	GLU	1	D	D	2 - 375	2 - 375
1	2	1	PRO	PRO	CL	CL	1	A	A - E	379 - 700	379
2	2	1	PRO	PRO	CL	CL	1	C	C - L	379 - 700	379
3	2	1	PRO	PRO	CL	CL	1	D	D - P	379 - 700	379
1	1	2	ILE	ILE	GLY	GLY	4	A	A	2 - 37	2 - 37
2	1	2	ILE	ILE	GLY	GLY	4	B	B	2 - 37	2 - 37
1	2	2	VAL	VAL	THR	THR	4	A	A	39 - 48	39 - 48
2	2	2	VAL	VAL	THR	THR	4	B	B	39 - 48	39 - 48
1	3	2	PHE	PHE	ALA	ALA	4	A	A	56 - 71	56 - 71
2	3	2	PHE	PHE	ALA	ALA	4	B	B	56 - 71	56 - 71
1	4	2	GLY	GLY	GLU	GLU	4	A	A	72 - 85	72 - 85
2	4	2	GLY	GLY	GLU	GLU	4	B	B	72 - 85	72 - 85
1	5	2	GLU	GLU	ALA	ALA	4	A	A	95 - 111	95 - 111
2	5	2	GLU	GLU	ALA	ALA	4	B	B	95 - 111	95 - 111
1	6	2	PHE	PHE	ASP	ASP	4	A	A	119 - 140	119 - 140
2	6	2	PHE	PHE	ASP	ASP	4	B	B	119 - 140	119 - 140
1	7	2	VAL	VAL	GLN	GLN	4	A	A	188 - 200	188 - 200
2	7	2	VAL	VAL	GLN	GLN	4	B	B	188 - 200	188 - 200
1	8	2	TRP	TRP	HIS	HIS	4	A	A	205 - 210	205 - 210
2	8	2	TRP	TRP	HIS	HIS	4	B	B	205 - 210	205 - 210
1	9	2	GLU	GLU	ALA	ALA	4	A	A	216 - 253	216 - 253
2	9	2	GLU	GLU	ALA	ALA	4	B	B	216 - 253	216 - 253
1	10	2	ARG	ARG	THR	THR	4	A	A	267 - 282	267 - 282
2	10	2	ARG	ARG	THR	THR	4	B	B	267 - 282	267 - 282
1	11	2	ARG	ARG	SER	SER	4	A	A	288 - 301	288 - 301
2	11	2	ARG	ARG	SER	SER	4	B	B	288 - 301	288 - 301
1	12	2	GLN	GLN	PRO	PRO	4	A	A	326 - 373	326 - 373
2	12	2	GLN	GLN	PRO	PRO	4	B	B	326 - 373	326 - 373
1	13	2	ASP	ASP	ASP	ASP	4	A	A	378 - 478	378 - 478
2	13	2	ASP	ASP	ASP	ASP	4	B	B	378 - 478	378 - 478
1	14	2	LEU	LEU	CL	CL	4	A	A - E	496 - 700	496
2	14	2	LEU	LEU	CL	CL	4	B	B - I	496 - 700	496
1	1	3	FAD	FAD	FAD	FAD	1	A	F	1513
2	1	3	FAD	FAD	FAD	FAD	1	B	J	1652
3	1	3	FAD	FAD	FAD	FAD	1	C	M	1513
4	1	3	FAD	FAD	FAD	FAD	1	D	Q	1513

NCS ensembles :

ID
1
2
3

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Protein , 1 types, 4 molecules ABCD

#1: Protein	TRYPTOPHAN 5-HALOGENASE / TRYPTOPHAN 5-HALOGENASE PYRH Mass: 58218.492 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: FAD AND TRYPTOPHAN IN CHAIN B, FAD IN OTHER THREE CHAINS Source: (gene. exp.) STREPTOMYCES RUGOSPORUS (bacteria) / Strain: LL-42D005 / Production host: PSEUDOMONAS FLUORESCENS (bacteria) / Strain (production host): BL915 / References: UniProt: A4D0H5

#1: Protein

TRYPTOPHAN 5-HALOGENASE / TRYPTOPHAN 5-HALOGENASE PYRH

Mass: 58218.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: FAD AND TRYPTOPHAN IN CHAIN B, FAD IN OTHER THREE CHAINS
Source: (gene. exp.)

STREPTOMYCES RUGOSPORUS (bacteria) / Strain: LL-42D005 / Production host:

PSEUDOMONAS FLUORESCENS (bacteria) / Strain (production host): BL915 / References: UniProt: A4D0H5

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Non-polymers , 5 types, 760 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#4: Chemical	ChemComp-TRP / TRYPTOPHAN / Tryptophan Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.62 % / Description: NONE
Crystal grow	pH: 6.2 Details: 0.05M SODIUM CACODYLATE BUFFER PH6.2, 1.4M LI2SO4 0.01M MGCL2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 113154 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 7 % / R_merge(I) obs: 0.09 / Net I/σ(I): 16.9
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.34 / Mean I/σ(I) obs: 3.7 / % possible all: 92.4

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0070	refinement
MOSFLM		data reduction
MOSFLM		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AQJ

2aqj

Resolution: 2.4→48.06 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.913 / SU B: 15.293 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2338	5684	5 %	RANDOM
R_work	0.19633	-	-	-
obs	0.19817	108080	98.27 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 20.538 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.72 Å²	0 Å²	0 Å²
2-	-	-0.72 Å²	0 Å²
3-	-	-	1.43 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→48.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15958	0	240	746	16944

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	16704
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.32	1.955	22701
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.832	5	1985
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.847	22.57	856
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.489	15	2609
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.586	15	167
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	2339
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	13107
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.445	1.5	9889
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.863	2	15847
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.543	3	6815
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.455	4.5	6854
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	3904	tight positional	0.06	0.05
1	2	C	3904	tight positional	0.05	0.05
1	3	D	3904	tight positional	0.04	0.05
3	1	A	53	tight positional	0.05	0.05
3	2	B	53	tight positional	0.05	0.05
3	3	C	53	tight positional	0.04	0.05
3	4	D	53	tight positional	0.03	0.05
2	1	A	2884	medium positional	0.24	0.5
2	2	B	2884	medium positional	0.24	0.5
1	1	A	3904	tight thermal	0.14	0.5
1	2	C	3904	tight thermal	0.11	0.5
1	3	D	3904	tight thermal	0.11	0.5
3	1	A	53	tight thermal	0.41	0.5
3	2	B	53	tight thermal	0.44	0.5
3	3	C	53	tight thermal	0.16	0.5
3	4	D	53	tight thermal	0.13	0.5
2	1	A	2884	medium thermal	1.12	2
2	2	B	2884	medium thermal	1.12	2

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.299	355	-
R_work	0.257	7043	-
obs	-	-	87.44 %

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	1.7452	0.3282	0.8171	1.1704	-0.293	1.5309	-0.1568	0.0827	0.0525	-0.048	-0.021	-0.0707	-0.0575	0.0744	0.1779	0.0778	-0.0246	-0.0601	0.063	0.0687	0.1131	-1.4784	35.1479	-26.4275
2	0.8904	0.0478	0.2927	1.5387	0.3112	0.7112	0.0419	0.0355	-0.113	0.0488	0.0177	-0.1376	0.0181	0.1495	-0.0596	0.2226	-0.0329	-0.1427	0.0886	0.0492	0.1297	1.1323	86.5375	-4.688
3	2.6646	0.3331	0.2329	0.87	-0.0951	1.2703	-0.1093	0.5439	0.2055	-0.2416	-0.0135	0.0464	-0.2111	0.0393	0.1227	0.2793	0.0124	-0.1055	0.1333	0.0456	0.0648	-26.8426	108.525	-23.9958
4	3.5451	0.8098	1.5511	1.3156	0.3708	1.4838	0.2964	0.7242	-0.93	-0.1059	0.016	-0.4747	0.4038	0.6398	-0.3124	0.2662	0.1808	-0.1309	0.398	-0.0029	0.5495	28.9148	9.1818	-18.9063

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 511
2	X-RAY DIFFRACTION	1	A	1513
3	X-RAY DIFFRACTION	2	B	1 - 511
4	X-RAY DIFFRACTION	2	B	1652
5	X-RAY DIFFRACTION	3	C	1 - 511
6	X-RAY DIFFRACTION	3	C	1513
7	X-RAY DIFFRACTION	4	D	1 - 511
8	X-RAY DIFFRACTION	4	D	1513

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