PDB-6d1o: FT_5 dioxygenase apoenzyme

ID or keywords:

Entry

Database: PDB / ID: 6d1o

Title

FT_5 dioxygenase apoenzyme

Components

(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

Keywords

OXIDOREDUCTASE / Alpha-ketoglutarate-dependent dioxygenase

Function / homology

Function and homology information

(R)-dichlorprop dioxygenase (2-oxoglutarate) / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Sphingobium herbicidovorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Rydel, T.J. / Halls, C.E.

Citation

Journal: Pest Manag. Sci. / Year: 2019
Title: Development of enzymes for robust aryloxyphenoxypropionate and synthetic auxin herbicide tolerance traits in maize and soybean crops.
Authors: Larue, C.T. / Goley, M. / Shi, L. / Evdokimov, A.G. / Sparks, O.C. / Ellis, C. / Wollacott, A.M. / Rydel, T.J. / Halls, C.E. / Van Scoyoc, B. / Fu, X. / Nageotte, J.R. / Adio, A.M. / Zheng, ...

History

Deposition	Apr 12, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jul 17, 2019	Group: Data collection / 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_author.identifier_ORCID
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6d1o.cif.gz	857.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6d1o.ent.gz	725.8 KB	Display	PDB format
PDBx/mmJSON format	6d1o.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/d1/6d1o ftp://data.pdbj.org/pub/pdb/validation_reports/d1/6d1o	HTTPS FTP

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Related structure data

Related structure data	6d0oC 6d3hC 6d3iC 6d3jC 6d3mC C: citing same article (ref.)
Similar structure data	6d0o-d 6d3h-1 6d3h-2 1oih-d 4toq-d 3bnm-d 6d3i-1 6d3j-1 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

Deposited unit

A: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

B: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

C: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

D: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

E: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

F: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

G: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

H: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

273 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

B: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

C: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

D: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

defined by author&software
136 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

F: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

G: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

H: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

defined by author&software
Evidence: gel filtration, light scattering
136 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.462, 200.326, 98.308
Angle α, β, γ (deg.)	90.00, 110.95, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-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
1	1	PHE	PHE	ARG	ARG	A	A	12 - 295	12 - 295
2	1	PHE	PHE	ARG	ARG	B	B	12 - 295	12 - 295
1	2	PHE	PHE	ALA	ALA	A	A	12 - 294	12 - 294
2	2	PHE	PHE	ALA	ALA	C	C	12 - 294	12 - 294
1	3	PHE	PHE	ALA	ALA	A	A	12 - 294	12 - 294
2	3	PHE	PHE	ALA	ALA	D	D	12 - 294	12 - 294
1	4	PHE	PHE	ARG	ARG	A	A	12 - 295	12 - 295
2	4	PHE	PHE	ARG	ARG	E	E	12 - 295	12 - 295
1	5	PHE	PHE	ARG	ARG	A	A	12 - 295	12 - 295
2	5	PHE	PHE	ARG	ARG	F	F	12 - 295	12 - 295
1	6	PHE	PHE	ARG	ARG	A	A	12 - 295	12 - 295
2	6	PHE	PHE	ARG	ARG	G	G	12 - 295	12 - 295
1	7	PHE	PHE	ARG	ARG	A	A	12 - 295	12 - 295
2	7	PHE	PHE	ARG	ARG	H	H	12 - 295	12 - 295
1	8	PHE	PHE	ALA	ALA	B	B	12 - 294	12 - 294
2	8	PHE	PHE	ALA	ALA	C	C	12 - 294	12 - 294
1	9	PHE	PHE	ARG	ARG	B	B	12 - 295	12 - 295
2	9	PHE	PHE	ARG	ARG	D	D	12 - 295	12 - 295
1	10	PHE	PHE	ARG	ARG	B	B	12 - 295	12 - 295
2	10	PHE	PHE	ARG	ARG	E	E	12 - 295	12 - 295
1	11	PHE	PHE	ARG	ARG	B	B	12 - 295	12 - 295
2	11	PHE	PHE	ARG	ARG	F	F	12 - 295	12 - 295
1	12	PHE	PHE	ARG	ARG	B	B	12 - 295	12 - 295
2	12	PHE	PHE	ARG	ARG	G	G	12 - 295	12 - 295
1	13	PHE	PHE	ARG	ARG	B	B	12 - 295	12 - 295
2	13	PHE	PHE	ARG	ARG	H	H	12 - 295	12 - 295
1	14	GLN	GLN	ARG	ARG	C	C	10 - 295	10 - 295
2	14	GLN	GLN	ARG	ARG	D	D	10 - 295	10 - 295
1	15	ARG	ARG	ARG	ARG	C	C	11 - 295	11 - 295
2	15	ARG	ARG	ARG	ARG	E	E	11 - 295	11 - 295
1	16	ARG	ARG	ARG	ARG	C	C	11 - 295	11 - 295
2	16	ARG	ARG	ARG	ARG	F	F	11 - 295	11 - 295
1	17	ARG	ARG	ARG	ARG	C	C	11 - 295	11 - 295
2	17	ARG	ARG	ARG	ARG	G	G	11 - 295	11 - 295
1	18	GLN	GLN	ARG	ARG	C	C	10 - 295	10 - 295
2	18	GLN	GLN	ARG	ARG	H	H	10 - 295	10 - 295
1	19	ARG	ARG	ARG	ARG	D	D	11 - 295	11 - 295
2	19	ARG	ARG	ARG	ARG	E	E	11 - 295	11 - 295
1	20	ARG	ARG	ARG	ARG	D	D	11 - 295	11 - 295
2	20	ARG	ARG	ARG	ARG	F	F	11 - 295	11 - 295
1	21	ARG	ARG	ARG	ARG	D	D	11 - 295	11 - 295
2	21	ARG	ARG	ARG	ARG	G	G	11 - 295	11 - 295
1	22	GLN	GLN	ARG	ARG	D	D	10 - 295	10 - 295
2	22	GLN	GLN	ARG	ARG	H	H	10 - 295	10 - 295
1	23	ARG	ARG	ARG	ARG	E	E	11 - 295	11 - 295
2	23	ARG	ARG	ARG	ARG	F	F	11 - 295	11 - 295
1	24	ARG	ARG	ARG	ARG	E	E	11 - 295	11 - 295
2	24	ARG	ARG	ARG	ARG	G	G	11 - 295	11 - 295
1	25	ARG	ARG	ARG	ARG	E	E	11 - 295	11 - 295
2	25	ARG	ARG	ARG	ARG	H	H	11 - 295	11 - 295
1	26	ARG	ARG	ARG	ARG	F	F	11 - 295	11 - 295
2	26	ARG	ARG	ARG	ARG	G	G	11 - 295	11 - 295
1	27	ARG	ARG	ARG	ARG	F	F	11 - 295	11 - 295
2	27	ARG	ARG	ARG	ARG	H	H	11 - 295	11 - 295
1	28	ARG	ARG	ALA	ALA	G	G	11 - 294	11 - 294
2	28	ARG	ARG	ALA	ALA	H	H	11 - 294	11 - 294

NCS ensembles :

#1: Protein	(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase / RdpA / (R)-dichlorprop/(R)-mecoprop dioxygenase / Alpha-ketoglutarate-dependent dioxygenase / ...RdpA / (R)-dichlorprop/(R)-mecoprop dioxygenase / Alpha-ketoglutarate-dependent dioxygenase / Dichlorprop/alpha-ketoglutarate-dioxygenase / Mecoprop/alpha-ketoglutarate-dioxygenase Mass: 34077.332 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: engineered variant Source: (gene. exp.) Sphingobium herbicidovorans (strain ATCC 700291 / DSM 11019 / NBRC 16415 / MH) (bacteria) Strain: ATCC 700291 / DSM 11019 / NBRC 16415 / MH / Gene: rdpA / Production host: Escherichia coli (E. coli) References: UniProt: Q8KSC8, (R)-dichlorprop dioxygenase (2-oxoglutarate)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase / RdpA / (R)-dichlorprop/(R)-mecoprop dioxygenase / Alpha-ketoglutarate-dependent dioxygenase / ...

Mass: 34077.332 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: engineered variant
Source: (gene. exp.)

Sphingobium herbicidovorans (strain ATCC 700291 / DSM 11019 / NBRC 16415 / MH) (bacteria)
Strain: ATCC 700291 / DSM 11019 / NBRC 16415 / MH / Gene: rdpA / Production host:

Escherichia coli (E. coli)
References: UniProt: Q8KSC8, (R)-dichlorprop dioxygenase (2-oxoglutarate)

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.38 Å³/Da / Density % sol: 48.25 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop Details: Crystal grew from Hampton Research SaltRx screen, condition C3: 2.0M sodium formate, 0.1M sodium acetate-pH 4.6.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→46.2 Å / Num. obs: 67790 / % possible obs: 97.6 % / Redundancy: 2.5 % / R_sym value: 0.059 / Net I/σ(I): 14.4
Reflection shell	Resolution: 2.7→2.75 Å / Redundancy: 2.5 % / Num. unique obs: 3120 / R_sym value: 0.301 / % possible all: 89.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→46.19 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.92 / SU B: 36.338 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24114	3438	5.1 %	RANDOM
R_work	0.21349	-	-	-
obs	0.21493	64352	97.48 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 72.032 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.93 Å²	0 Å²	0.1 Å²
2-	-	1.44 Å²	0 Å²
3-	-	-	0.32 Å²

Refinement step

Cycle: 1 / Resolution: 2.7→46.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17037	0	0	173	17210

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	17495
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	15709
X-RAY DIFFRACTION	r_angle_refined_deg	2.267	1.944	23860
X-RAY DIFFRACTION	r_angle_other_deg	1.241	3	36356
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.766	5	2115
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.07	23.357	855
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.739	15	2698
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.298	15	136
X-RAY DIFFRACTION	r_chiral_restr	0.137	0.2	2617
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	19545
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3747
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	1.874	2.503	8526
X-RAY DIFFRACTION	r_mcbond_other	1.874	2.503	8525
X-RAY DIFFRACTION	r_mcangle_it	3.22	3.739	10619
X-RAY DIFFRACTION	r_mcangle_other	3.22	3.739	10620
X-RAY DIFFRACTION	r_scbond_it	1.538	2.636	8969
X-RAY DIFFRACTION	r_scbond_other	1.538	2.636	8970
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.621	3.889	13242
X-RAY DIFFRACTION	r_long_range_B_refined	6.097	28.482	18882
X-RAY DIFFRACTION	r_long_range_B_other	6.096	28.477	18881
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	17272	0.05
1	2	B	17272	0.05
2	1	A	16980	0.07
2	2	C	16980	0.07
3	1	A	16950	0.06
3	2	D	16950	0.06
4	1	A	17152	0.05
4	2	E	17152	0.05
5	1	A	17010	0.06
5	2	F	17010	0.06
6	1	A	16822	0.08
6	2	G	16822	0.08
7	1	A	16748	0.08
7	2	H	16748	0.08
8	1	B	16872	0.07
8	2	C	16872	0.07
9	1	B	16928	0.07
9	2	D	16928	0.07
10	1	B	17046	0.05
10	2	E	17046	0.05
11	1	B	16910	0.06
11	2	F	16910	0.06
12	1	B	16748	0.08
12	2	G	16748	0.08
13	1	B	16644	0.08
13	2	H	16644	0.08
14	1	C	17288	0.07
14	2	D	17288	0.07
15	1	C	17094	0.07
15	2	E	17094	0.07
16	1	C	16986	0.06
16	2	F	16986	0.06
17	1	C	16892	0.09
17	2	G	16892	0.09
18	1	C	16840	0.09
18	2	H	16840	0.09
19	1	D	17078	0.07
19	2	E	17078	0.07
20	1	D	16954	0.06
20	2	F	16954	0.06
21	1	D	16840	0.08
21	2	G	16840	0.08
22	1	D	16844	0.08
22	2	H	16844	0.08
23	1	E	17282	0.05
23	2	F	17282	0.05
24	1	E	16922	0.08
24	2	G	16922	0.08
25	1	E	16806	0.08
25	2	H	16806	0.08
26	1	F	16784	0.08
26	2	G	16784	0.08
27	1	F	16716	0.08
27	2	H	16716	0.08
28	1	G	17730	0.06
28	2	H	17730	0.06

LS refinement shell

Resolution: 2.701→2.771 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.343	241	-
R_work	0.329	4256	-
obs	-	-	88.7 %

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	0.9956	-0.6474	0.812	2.475	-0.0852	0.8015	-0.3807	-0.2101	0.0982	0.0962	0.2965	-0.052	-0.1313	-0.1438	0.0841	1.2195	0.0359	-0.1348	0.0579	-0.0228	0.2956	-6.614	31.261	30.423
2	1.0628	-0.6676	-0.8536	2.5418	-0.083	0.9198	-0.4156	-0.21	-0.0939	0.0846	0.3324	0.0312	0.1501	0.1163	0.0831	1.2339	0.0398	0.1309	0.0613	0.0211	0.2986	6.664	-18.982	30.403
3	1.106	0.626	0.5517	3.8673	0.3277	0.4112	-0.2578	-0.1433	-0.099	0.058	0.3928	0.5366	0.0592	-0.1317	-0.135	1.054	0.134	0.1842	0.1678	0.2212	0.3024	-16.624	-13.834	52.537
4	0.9149	0.506	-0.5769	3.7679	-0.1845	0.5702	-0.2498	-0.1207	0.1422	0.0797	0.3828	-0.5268	-0.0231	0.1828	-0.133	1.0597	0.1273	-0.1937	0.1734	-0.1988	0.2965	16.571	26.251	52.524
5	0.3694	0.3176	0.6741	5.5083	-0.5703	1.5828	0.1521	-0.0979	-0.0766	0.4705	-0.0589	0.2019	0.1449	-0.2449	-0.0932	0.8631	-0.0691	-0.0387	0.0843	0.0017	0.2825	6.175	31.55	99.688
6	0.4065	-0.3987	-0.6732	5.4202	-0.5021	1.4436	0.1959	0.1148	0.0649	-0.4423	-0.1244	0.1903	-0.167	-0.2187	-0.0716	0.874	0.069	0.0416	0.0762	-0.0053	0.2799	6.343	81.037	84.015
7	0.4588	0.451	-0.2354	3.68	1.3468	1.101	0.1439	0.0597	-0.0113	0.5777	-0.3378	0.6609	0.0135	-0.1422	0.1939	1.0044	-0.0242	0.2347	0.0901	-0.1371	0.5046	-14.75	76.583	107.57
8	0.3015	-0.4143	0.1866	3.2847	1.3029	1.3671	0.1068	-0.0608	0.0235	-0.5838	-0.2845	0.6757	-0.0197	-0.169	0.1777	1.0077	-0.0019	-0.2397	0.0853	-0.143	0.5231	-14.988	35.67	76.2

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	12 - 295
2	X-RAY DIFFRACTION	2	B	12 - 295
3	X-RAY DIFFRACTION	3	C	10 - 295
4	X-RAY DIFFRACTION	4	D	10 - 295
5	X-RAY DIFFRACTION	5	E	11 - 295
6	X-RAY DIFFRACTION	6	F	11 - 295
7	X-RAY DIFFRACTION	7	G	11 - 295
8	X-RAY DIFFRACTION	8	H	9 - 295

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