PDB-6kd9: Binding pose 1 of 2-CF3 bound AsqJ complex

ID or keywords:

Entry

Database: PDB / ID: 6kd9

Title

Binding pose 1 of 2-CF3 bound AsqJ complex

Components

Iron/alpha-ketoglutarate-dependent dioxygenase asqJ

Keywords

OXIDOREDUCTASE / 2-CF3 /

epoxidation

Function / homology

Function and homology information

(-)-cyclopenine synthase /

dioxygenase activity /

metal ion binding
Similarity search - Function

Biological species

Emericella nidulans (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.44 Å

Authors

Liao, H.J. / Chan, N.L.

Citation

Journal: J.Am.Chem.Soc. / Year: 2020
Title: Binding pose 1 of 2-CF3 bound AsqJ complex
Authors: Liao, H.J. / Chan, N.L.

History

Deposition	Jul 1, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2	Mar 20, 2024	Group: Source and taxonomy / Category: entity_src_gen

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6kd9.cif.gz	243.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6kd9.ent.gz	196.4 KB	Display	PDB format
PDBx/mmJSON format	6kd9.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/kd/6kd9 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/6kd9	HTTPS FTP

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Related structure data

Related structure data	5y7rS S: Starting model for refinement
Similar structure data	5dax-1 3bit-1 1s9c-1 5oa4-1 5c4f-1 1eny-1 4km3-d 3pfb-d 2r6u-d 2dzw-d 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

B: Iron/alpha-ketoglutarate-dependent dioxygenase asqJ

F: Iron/alpha-ketoglutarate-dependent dioxygenase asqJ

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	66.755, 73.352, 121.434
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Iron/alpha-ketoglutarate-dependent dioxygenase asqJ / 4'-methoxyviridicatin/aspoquinolone biosynthesis cluster protein asqJ / Aspoquinolone biosynthesis protein J Mass: 36107.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold) Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: asqJ, AN9227 / Production host: Escherichia coli (E. coli) References: UniProt: Q5AR53, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical	ChemComp-FE / FE (III) ION / Iron Mass: 55.845 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: Fe
#3: Chemical	ChemComp-CV3 / (3~{Z})-4-methyl-3-[[4-(trifluoromethyl)phenyl]methylidene]-1~{H}-1,4-benzodiazepine-2,5-dione Mass: 346.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₁₃F₃N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SIN / SUCCINIC ACID / Succinic acid Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.25 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.6 M potassium sodium tartrate tetrahydrate, 0.1 M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.44→30 Å / Num. obs: 22286 / % possible obs: 99.8 % / Redundancy: 4.5 % / Net I/σ(I): 15.9
Reflection shell	Resolution: 2.45→2.54 Å / Num. unique obs: 1702

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5y7r

5y7r

Resolution: 2.44→29.472 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 42.89

	R_factor	Num. reflection	% reflection
R_free	0.2855	1108	5 %
R_work	0.2176	-	-
obs	0.2211	22174	97.15 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.44→29.472 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4436	0	68	41	4545

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4610
X-RAY DIFFRACTION	f_angle_d	1.086	6286
X-RAY DIFFRACTION	f_dihedral_angle_d	7.662	3774
X-RAY DIFFRACTION	f_chiral_restr	0.061	738
X-RAY DIFFRACTION	f_plane_restr	0.009	817

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 (%)
2.4402-2.5512	0.3365	121	0.2809	2130	X-RAY DIFFRACTION	81
2.5512-2.6857	0.3769	147	0.2801	2662	X-RAY DIFFRACTION	100
2.6857-2.8538	0.3502	141	0.2822	2657	X-RAY DIFFRACTION	100
2.8538-3.0739	0.3507	128	0.2671	2690	X-RAY DIFFRACTION	100
3.0739-3.3829	0.3341	141	0.2447	2682	X-RAY DIFFRACTION	100
3.3829-3.8715	0.2907	156	0.2083	2680	X-RAY DIFFRACTION	100
3.8715-4.8741	0.2386	127	0.179	2754	X-RAY DIFFRACTION	100
4.8741-29.474	0.2395	147	0.1904	2811	X-RAY DIFFRACTION	98

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	1.8038	0.9031	-1.7702	1.0053	-1.507	2.4343	-0.0256	-0.0024	-0.0434	-0.3165	-0.1216	-0.0907	0.9508	1.2241	0.13	0.4585	0.098	-0.0721	0.4598	-0.1006	0.366	-13.6194	-8.0394	-27.336
2	8.2902	-4.7534	-5.1793	7.2528	5.092	6.2263	-0.4513	-0.1646	-0.0602	0.8241	-0.0265	0.3036	0.0339	-0.2776	0.4336	0.5161	-0.0303	0.0044	0.4527	-0.0414	0.3566	-24.8082	-7.5327	-5.3604
3	0.9424	1.4136	0.0349	7.078	-0.2121	4.7062	-0.3112	-0.7957	1.0861	-0.0321	0.0955	1.4596	-0.995	-1.0418	0.145	0.5571	0.0935	-0.0352	0.4823	-0.2051	0.8104	-34.0397	6.7309	-10.9863
4	8.5339	3.4853	-5.5343	8.6454	-3.4252	4.1787	0.0154	-0.5364	-0.7722	0.4636	-0.6851	-0.7965	-1.1652	0.0202	0.5641	0.4126	0.067	-0.0661	0.3061	-0.0709	0.3528	-11.0855	-0.4567	-14.2393
5	0.9481	1.8692	-0.3852	3.5806	-1.0762	1.705	-0.2401	-0.0105	0.3599	-0.5326	0.1787	0.7092	0.3638	-0.3338	0.0642	0.5178	-0.0083	-0.1507	0.3949	-0.107	0.4341	-22.6874	6.8408	-24.0445
6	4.8658	0.3622	0.364	2.1371	1.1769	5.9137	-0.3041	1.3616	0.0604	-0.7805	0.4979	0.5525	-0.5513	-0.5828	-0.2509	0.6231	-0.118	-0.223	0.6737	-0.037	0.4586	-28.2091	-2.9937	-32.5408
7	2.6344	0.1764	-0.5757	1.7242	-1.7295	1.7512	-0.1578	0.1331	-0.0318	-0.4629	0.1545	0.4954	0.0845	-0.4208	0.0349	0.5561	0.0657	-0.1379	0.3527	-0.1129	0.4492	-26.7893	-4.8139	-22.7859
8	3.3458	-0.2739	-1.4674	3.3249	-2.1457	2.3223	0.086	-0.2999	0.2114	-0.0318	-0.1575	0.5063	0.0748	-0.2883	0.1096	0.3145	-0.0507	-0.0699	0.3601	-0.1414	0.3628	-14.3862	10.2854	-7.178
9	1.7842	1.6007	-2.1316	5.1896	-2.4387	2.8231	0.6351	-0.7274	0.2779	0.0453	-0.5792	-0.2285	-0.3963	0.0758	-0.054	0.3107	0.0017	-0.1379	0.4734	-0.13	0.3902	-5.7803	18.7036	-14.2027
10	0.8797	0.7827	-1.3478	2.3521	-3.9013	6.4626	1.362	-1.2459	-0.0476	2.819	-1.2465	-0.3824	-0.9435	1.1893	0.0408	1.0743	-0.3241	-0.137	1.1231	0.003	0.4638	-5.7135	13.1112	-0.7254
11	5.0494	0.2336	2.0987	2.4454	-4.2964	9.3643	0.0867	0.3201	0.3146	-0.3048	0.1429	0.7989	-0.1418	-0.0957	-0.2172	0.9161	0.1086	-0.4424	0.5055	-0.0489	0.9389	-19.7499	44.7477	-27.3326
12	7.8024	-4.8425	5.3794	8.3637	-4.7823	6.7282	-0.8659	-1.488	0.9519	1.2741	0.5297	0.0339	-1.5451	-0.1525	0.3662	0.6597	-0.1052	0.0329	0.7819	-0.3626	0.6413	-8.5529	44.2431	-5.3544
13	3.944	1.2876	-3.3943	0.5413	-1.0277	2.9584	0.5609	-0.1025	-0.0878	0.3683	-0.3684	-0.3425	-0.7465	-0.018	-0.119	0.4396	-0.0465	-0.1528	0.711	-0.1971	0.5054	0.6397	29.959	-10.9906
14	7.3689	2.0133	2.2145	2.1805	0.6283	3.5	0.3332	-0.4687	0.6977	-0.3084	-0.5528	1.1076	-0.0831	-0.5719	0.2237	0.4563	0.0418	-0.2059	0.4845	-0.1354	0.7732	-19.4388	34.2594	-15.9566
15	0.7435	1.5279	-0.4685	3.3473	-0.3475	0.7076	0.0085	-0.1497	0.1901	-0.5859	-0.166	0.2249	0.3365	-0.1496	0.1658	0.6624	0.1514	-0.2097	0.4685	-0.0309	0.4386	-8.3746	29.552	-26.7307
16	5.9622	2.1624	-0.4625	5.1867	-0.608	5.908	-0.1347	-0.2177	-0.3095	-1.1402	-0.3228	-0.155	-0.6782	0.0745	0.5415	0.6892	0.1362	-0.248	0.4379	-0.0235	0.5039	-5.1351	39.649	-32.512
17	3.8343	0.287	-0.8793	2.4027	-1.4892	1.0972	-0.0604	-0.0907	0.414	0.002	-0.0322	0.2982	-0.3216	0.1192	0.0897	0.5477	0.0255	-0.1459	0.4312	-0.1383	0.4793	-6.5791	41.4841	-22.7824
18	5.1078	-1.9094	-0.5981	6.0588	-2.4221	2.9516	0.1909	-1.0252	-0.0872	0.3994	-0.2485	0.6299	-0.1451	-0.2805	0.0775	0.4638	-0.0591	0.0289	0.6251	-0.2235	0.5305	-18.9813	26.4393	-7.1871
19	6.8747	0.7723	-1.1399	9.0222	-5.6047	8.0996	0.3149	0.766	-0.5536	-0.105	0.8048	0.7736	-0.6949	-0.4689	-0.9385	0.4664	0.1475	-0.0622	0.5948	-0.2047	0.6364	-27.5864	17.973	-14.2285
20	0.0212	-0.3776	-0.1159	6.9175	1.5787	1.2063	-0.1855	-0.4746	0.237	0.7185	-0.1926	0.2431	0.105	-0.0141	-0.0379	-0.0588	0.4412	0.2275	0.4871	-0.56	1.2072	-27.7206	23.5245	-0.7197

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 9 through 40 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 41 through 56 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 57 through 87 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 88 through 108 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 109 through 161 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 162 through 191 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 192 through 232 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 233 through 259 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 260 through 279 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 280 through 295 )
11	X-RAY DIFFRACTION	11	chain 'F' and (resid 9 through 40 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 41 through 56 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 57 through 87 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 88 through 124 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 125 through 161 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 162 through 191 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 192 through 232 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 233 through 259 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 260 through 279 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 280 through 295 )

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