PDB-2aqj: The structure of tryptophan 7-halogenase (PrnA) suggests a mechan...

ID or keywords:

Entry

Database: PDB / ID: 2aqj

Title

The structure of tryptophan 7-halogenase (PrnA) suggests a mechanism for regioselective chlorination

Components

tryptophan halogenase, PrnA

Keywords

BIOSYNTHETIC PROTEIN / tryptophan 7-halogenase / flavin-dependent halogenase / helical bundle / sandwiched sheets / Structural Genomics / Scottish Structural Proteomics Facility / SSPF

Function / homology

Function and homology information

tryptophan 7-halogenase / antibiotic biosynthetic process / monooxygenase activity / nucleotide binding
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Dong, C. / Flecks, S. / Unversucht, S. / Haupt, C. / Van Pee, K.-H. / Naismith, J.H. / Scottish Structural Proteomics Facility (SSPF)

Citation

Journal: Science / Year: 2005
Title: Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination.
Authors: Dong, C. / Flecks, S. / Unversucht, S. / Haupt, C. / van Pee, K.H. / Naismith, J.H.

History

Deposition	Aug 18, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 4, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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Validation report

Summary document	2aqj_validation.pdf.gz	687.9 KB	Display	wwPDB validaton report
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Data in XML	2aqj_validation.xml.gz	12.8 KB	Display
Data in CIF	2aqj_validation.cif.gz	20.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aq/2aqj ftp://data.pdbj.org/pub/pdb/validation_reports/aq/2aqj	HTTPS FTP

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Related structure data

Related structure data	2apgC 2ar8C 2ardC C: citing same article (ref.)
Similar structure data	2apg-1 2ar8-1 2ard-1 6lt7-d 6kyj-3 3v05-d 6kyi-d 1z4u-2 4rg7-d 2x4p-d 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 halogenase, PrnA

hetero molecules

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

1

A: tryptophan halogenase, PrnA

hetero molecules

A: tryptophan halogenase, PrnA

hetero molecules

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

Unit cell

Length a, b, c (Å)	67.630, 67.630, 276.027
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-764- HOH

#1: Protein	tryptophan halogenase, PrnA Mass: 61146.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: prnA / Plasmid: pPEH14 / Production host: Pseudomonas fluorescens (bacteria) / Strain (production host): BL915 / References: UniProt: P95480
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-TRP / TRYPTOPHAN Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂
#4: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.6 Å³/Da / Density % sol: 52.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 8% PEG20000, 0.1M Mes pH 6.5, 20mM tryptophan, VAPOR DIFFUSION, SITTING DROP, temperature 293 K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-1 / Wavelength: 0.934, 0.9796, 0.9798, 0.9252

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2003

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.934	1
2	0.9796	1
3	0.9798	1
4	0.9252	1

Reflection

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	R_sym value	D res high (Å)	D res low (Å)	% possible obs
13.1	1	8.2	15243	0.081	0.081	2.9	54.57	100
4.4	2	10	16587	0.061	0.061	2.8	54.5	98.9
5	3	8	15238	0.078	0.078	2.9	54.57	100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
12.97	55.21	98.8	1	0.03	0.03	9.5
9.17	12.97	100	1	0.027	0.027	11.4
7.49	9.17	100	1	0.031	0.031	11.9
6.48	7.49	100	1	0.052	0.052	12.3
5.8	6.48	100	1	0.083	0.083	12.6
5.29	5.8	100	1	0.076	0.076	12.8
4.9	5.29	100	1	0.06	0.06	12.8
4.59	4.9	100	1	0.055	0.055	13
4.32	4.59	100	1	0.056	0.056	13.2
4.1	4.32	100	1	0.062	0.062	13
3.91	4.1	100	1	0.074	0.074	13.3
3.74	3.91	100	1	0.082	0.082	13.3
3.6	3.74	100	1	0.097	0.097	13.3
3.47	3.6	100	1	0.116	0.116	13.4
3.35	3.47	100	1	0.144	0.144	13.3
3.24	3.35	100	1	0.164	0.164	13.5
3.15	3.24	100	1	0.204	0.204	13.4
3.06	3.15	100	1	0.25	0.25	13.5
2.98	3.06	100	1	0.332	0.332	13.5
2.9	2.98	100	1	0.405	0.405	13.5
12.52	55.19	95.1	2	0.028	0.028	3.5
8.85	12.52	98.4	2	0.025	0.025	4
7.23	8.85	98.6	2	0.026	0.026	4.3
6.26	7.23	99.4	2	0.046	0.046	4.3
5.6	6.26	99.1	2	0.057	0.057	4.4
5.11	5.6	99.6	2	0.055	0.055	4.4
4.73	5.11	99.7	2	0.044	0.044	4.5
4.43	4.73	99.7	2	0.042	0.042	4.5
4.17	4.43	99.8	2	0.046	0.046	4.4
3.96	4.17	99.9	2	0.051	0.051	4.6
3.78	3.96	100	2	0.06	0.06	4.6
3.61	3.78	100	2	0.066	0.066	4.5
3.47	3.61	100	2	0.085	0.085	4.6
3.35	3.47	100	2	0.098	0.098	4.5
3.23	3.35	100	2	0.115	0.115	4.6
3.13	3.23	100	2	0.143	0.143	4.6
3.04	3.13	100	2	0.176	0.176	4.6
2.95	3.04	100	2	0.248	0.248	4.6
2.87	2.95	100	2	0.301	0.301	4.6
2.8	2.87	88.7	2	0.36	0.36	3
12.97	55.27	98.2	3	0.026	0.026	3.7
9.17	12.97	99.8	3	0.026	0.026	4.2
7.49	9.17	100	3	0.027	0.027	4.6
6.48	7.49	100	3	0.038	0.038	4.7
5.8	6.48	100	3	0.057	0.057	4.8
5.29	5.8	100	3	0.061	0.061	4.8
4.9	5.29	100	3	0.063	0.063	4.9
4.59	4.9	100	3	0.055	0.055	4.9
4.32	4.59	100	3	0.05	0.05	5
4.1	4.32	99.9	3	0.057	0.057	5
3.91	4.1	99.9	3	0.07	0.07	5
3.74	3.91	100	3	0.075	0.075	5.1
3.6	3.74	100	3	0.092	0.092	5
3.47	3.6	100	3	0.116	0.116	5.1
3.35	3.47	100	3	0.138	0.138	5.1
3.24	3.35	100	3	0.155	0.155	5.1
3.15	3.24	100	3	0.191	0.191	5
3.06	3.15	100	3	0.239	0.239	5.2
2.98	3.06	100	3	0.311	0.311	5.1
2.9	2.98	100	3	0.37	0.37	5.1

Reflection

Resolution: 1.8→54.66 Å / Num. all: 57128 / Num. obs: 57013 / % possible obs: 93 % / Observed criterion σ(F): 2.11 / Observed criterion σ(I): 2.3 / Redundancy: 9.1 % / B_iso Wilson estimate: 25.52 Å² / R_merge(I) obs: 0.071 / R_sym value: 0.071 / Net I/σ(I): 6.4

Reflection shell

Resolution: 1.8→1.9 Å / % possible obs: 68.8 % / Redundancy: 5.2 % / R_merge(I) obs: 0.337 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 5997 / Num. unique all: 5997 / R_sym value: 0.337 / % possible all: 93

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9796	5.87	-8.13
1	3 wavelength	2	0.9798	2.57	-10.44
1	3 wavelength	3	0.9252	3.15	-2.94

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	60	0.579	0.227	0.119	0.968
2	Se	60	0.224	0.947	0.074	1.003
3	Se	60	0.891	0.233	0.052	0.872
4	Se	60	0.345	0.135	0.103	0.896
5	Se	60	0.24	0.078	0.047	0.887
6	Se	60	0.309	0.249	0.059	0.95
7	Se	56.059	0.883	0.029	0.079	0.886
8	Se	60	0.786	0.141	0.019	0.742
9	Se	60	0.014	0.894	0.093	0.781
10	Se	60	0.076	0.983	0.121	0.822
11	Se	60	0.015	0.396	0.052	0.506

Phasing dm

FOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0.67 / Reflection: 14782 / Reflection acentric: 11918 / Reflection centric: 2864

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8.3-19.977	0.94	0.96	0.91	695	391	304
5.2-8.3	0.9	0.92	0.84	2088	1505	583
4.1-5.2	0.87	0.88	0.82	2533	2006	527
3.6-4.1	0.76	0.78	0.71	2504	2056	448
3.1-3.6	0.54	0.55	0.49	4326	3680	646
2.9-3.1	0.31	0.31	0.27	2636	2280	356

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Processing

Software

Name	Version	Classification
SCALA		data scaling
SOLVE	2.03	phasing
RESOLVE	2.03	phasing
REFMAC		refinement
PDB_EXTRACT	1.7	data extraction
MOSFLM		data reduction
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MAD / Resolution: 1.8→54.66 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.953 / SU B: 5.48 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.202	2857	5.1 %	RANDOM
R_work	0.168	-	-	-
all	0.169	57013	-	-
obs	0.167	56573	93.12 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 29.429 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.24 Å²	0 Å²	0 Å²
2-	-	0.24 Å²	0 Å²
3-	-	-	-0.49 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→54.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4162	0	69	393	4624

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	4352
X-RAY DIFFRACTION	r_angle_refined_deg	1.478	1.961	5919
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.099	5	516
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.683	23.194	216
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.857	15	687
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.862	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	618
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3394
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	2329
X-RAY DIFFRACTION	r_nbtor_refined	0.317	0.2	3021
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	429
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.247	0.2	67
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.128	0.2	25
X-RAY DIFFRACTION	r_mcbond_it	1.099	1.5	2633
X-RAY DIFFRACTION	r_mcangle_it	1.67	2	4162
X-RAY DIFFRACTION	r_scbond_it	2.287	3	2053
X-RAY DIFFRACTION	r_scangle_it	3.371	4.5	1757
X-RAY DIFFRACTION	r_rigid_bond_restr	1.512	3	4686
X-RAY DIFFRACTION	r_sphericity_free	6.435	3	394
X-RAY DIFFRACTION	r_sphericity_bonded	2.48	3	4231

LS refinement shell

Resolution: 1.8→1.847 Å / R_factor R_free error: 0.01 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.272	150	-
R_work	0.194	2748	-
all	-	2898	-
obs	-	31170	65.88 %

Refinement TLS params.

Method: refined / Origin x: 10.247 Å / Origin y: 6.789 Å / Origin z: 20.143 Å

	11	12	13	21	22	23	31	32	33
T	-0.0855 Å²	-0.0125 Å²	-0.0025 Å²	-	0.0864 Å²	-0.0564 Å²	-	-	-0.0991 Å²
L	2.2919 °²	-0.7068 °²	-0.2246 °²	-	0.4174 °²	0.2489 °²	-	-	0.848 °²
S	0.0717 Å °	-0.3617 Å °	-0.0203 Å °	-0.0297 Å °	0.0998 Å °	-0.0174 Å °	0.0273 Å °	0.1469 Å °	-0.1714 Å °

Refinement TLS group

Selection: ALL

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