PDB-4ttb: Crystal structure of homo sapiens IODOTYROSINE DEIODINASE (IYD) b...

ID or keywords:

Entry

Database: PDB / ID: 4ttb

Title

Crystal structure of homo sapiens IODOTYROSINE DEIODINASE (IYD) bound to FMN

Components

Iodotyrosine dehalogenase 1

Iodotyrosine deiodinase

Keywords

OXIDOREDUCTASE /

FLAVOPROTEIN /

MEMBRANE /

TRANSMEMBRANE /

DEHALOGENASE / IODIDE SALVAGE / FMN / MONO-IODOTYROSINE /

NADP

Function / homology

Function and homology information

iodotyrosine deiodinase /

iodotyrosine deiodinase activity / Thyroxine biosynthesis / thyroid hormone metabolic process / tyrosine metabolic process / cytoplasmic vesicle membrane / FMN binding /

oxidoreductase activity /

nucleoplasm /

plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.447 Å

Authors

Chuenchor, W. / Hu, J. / Rokita, S.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2015
Title: A Switch between One- and Two-electron Chemistry of the Human Flavoprotein Iodotyrosine Deiodinase Is Controlled by Substrate.
Authors: Hu, J. / Chuenchor, W. / Rokita, S.E.

History

Deposition	Jun 20, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 14, 2015	Group: Database references
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ttb.cif.gz	175.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4ttb.ent.gz	138.7 KB	Display	PDB format
PDBx/mmJSON format	4ttb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tt/4ttb ftp://data.pdbj.org/pub/pdb/validation_reports/tt/4ttb	HTTPS FTP

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Related structure data

Related structure data	4ttcC 3to0S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6l5n-1 3gb5-1 3gkr-d 4rcf-d 1wmk-4 6kji-2 2uyh-d 3go2-d 2gga-d 2vwh-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
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Iodotyrosine dehalogenase 1

B: Iodotyrosine dehalogenase 1

hetero molecules

62.2 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)	72.892, 72.892, 95.515
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	Iodotyrosine dehalogenase 1 / Iodotyrosine deiodinase / IYD-1 Mass: 30655.057 Da / Num. of mol.: 2 / Fragment: UNP residues 32-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IYD, C6orf71, DEHAL1 / Plasmid: pET28-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2DE3 / References: UniProt: Q6PHW0, EC: 1.22.1.1
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.2 % / Description: Cubic crystal
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05 M ammonium sulfate, 25% Pentaerythritol ethoxylate, 50 mM BISTRIS PH range: 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: Single wavelength
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.447→50 Å / Num. all: 20957 / Num. obs: 20957 / % possible obs: 100 % / Redundancy: 8.2 % / R_sym value: 0.061 / Net I/σ(I): 33.8
Reflection shell	Resolution: 2.447→2.54 Å / Redundancy: 7.6 % / R_merge(I) obs: 0.613 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
Coot		model building
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3TO0

3to0

Resolution: 2.447→38.086 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2026	1066	5.12 %	Random selection
R_work	0.1926	-	-	-
obs	0.1932	20800	99.34 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.447→38.086 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3032	0	62	42	3136

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3175
X-RAY DIFFRACTION	f_angle_d	1.142	4325
X-RAY DIFFRACTION	f_dihedral_angle_d	12.778	1193
X-RAY DIFFRACTION	f_chiral_restr	0.075	502
X-RAY DIFFRACTION	f_plane_restr	0.006	537

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 (%)
2.447-2.558	0.3051	130	0.2966	2452	X-RAY DIFFRACTION	98
2.558-2.6928	0.2642	133	0.269	2463	X-RAY DIFFRACTION	99
2.6928-2.8615	0.2546	129	0.2387	2447	X-RAY DIFFRACTION	99
2.8615-3.0823	0.2216	138	0.2445	2469	X-RAY DIFFRACTION	100
3.0823-3.3924	0.2118	136	0.2126	2451	X-RAY DIFFRACTION	99
3.3924-3.8828	0.2259	130	0.1909	2501	X-RAY DIFFRACTION	100
3.8828-4.8903	0.1532	138	0.1562	2484	X-RAY DIFFRACTION	100
4.8903-38.0907	0.1871	132	0.1696	2467	X-RAY DIFFRACTION	99

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	4.2232	-2.5986	1.2268	7.4268	-4.9324	3.4895	0.3348	0.3682	0.1838	0.3691	0.3764	-0.2703	-0.8612	-0.3451	0.1443	1.3994	-0.025	-0.0205	1.0375	-0.2464	0.628	-19.8304	17.599	18.2265
2	4.7669	-2.0678	-1.5467	5.6015	2.999	8.6352	0.3694	0.2813	1.0509	-0.2743	-0.0196	-1.5489	-1.7779	-0.5857	-0.1044	0.6936	-0.064	-0.052	0.409	0.0955	0.6269	-20.8158	22.8573	-2.6046
3	4.3505	-1.6408	-0.2843	2.9872	0.3946	3.4752	-0.0142	0.7336	-0.1109	0.1533	-0.0201	-0.3429	0.5434	1.4067	0.164	0.3695	-0.0682	-0.0124	0.5515	-0.0271	0.4958	-7.5935	5.5431	-6.5271
4	3.1628	-0.8069	1.3053	3.7423	-0.2105	4.2855	-0.0182	-0.6018	-0.4145	0.3326	0.0174	0.2248	2.0701	0.6281	0.1541	1.0925	0.0585	0.0243	0.3064	0.0703	0.5305	-13.0818	-2.9418	5.2438
5	4.043	-5.0704	1.0964	8.3571	1.0168	3.55	0.3322	0.4295	-1.5659	-0.2153	0.28	1.1119	1.2416	0.8396	1.9197	2.1115	0.6265	0.1476	0.8051	-0.1849	0.6015	-7.7749	-13.0388	-14.2165
6	2.3468	0.4205	-0.6275	3.241	-0.1595	3.3379	0.0153	1.3355	-1.2109	-0.4967	0.5764	0.3384	1.6752	0.0953	0.1496	1.2324	0.1323	0.0329	0.8616	-0.2071	0.6377	-11.4648	-8.1564	-19.5014
7	4.1674	-1.6692	-0.5086	2.5272	0.2272	3.6055	-0.3949	0.3206	-0.6681	0.2465	0.1445	0.4437	2.2313	-0.0979	0.1556	1.0521	-0.093	0.0634	0.3133	-0.0546	0.5195	-15.5915	-3.6635	-3.0129
8	3.857	0.4547	-1.7206	2.7717	-2.1412	5.7737	-0.3136	-0.6161	-1.8701	0.9232	0.024	0.1952	2.1735	0.33	0.0196	1.6681	0.1302	-0.0249	0.3024	-0.1643	0.3363	-12.9193	-8.9594	-1.5565
9	7.7787	-2.134	-1.4127	1.7105	0.8025	6.9597	0.1673	1.7606	0.3447	-0.0502	-0.315	0.0335	-0.1621	-1.2422	0.1309	0.4629	-0.0669	-0.0709	0.7554	0.0377	0.4341	-24.6764	11.7959	-13.857
10	3.5679	0.159	-2.1073	1.0289	-0.3178	2.2083	0.8036	-0.2885	-0.3155	0.9457	0.1422	0.3093	-0.1585	0.562	-0.3361	1.0889	-0.2294	0.135	1.222	0.1194	0.8374	-11.359	12.7571	-18.8349
11	6.5971	-0.9496	-3.8629	3.7822	0.707	2.4493	-0.1554	-0.275	1.5749	0.3234	0.5189	-0.5637	-0.2892	1.6711	-0.131	0.5369	-0.2217	-0.1141	0.6729	-0.0247	0.6014	-6.3554	14.4541	1.9958
12	2.9017	-0.655	0.4649	2.6733	0.069	8.1733	-0.3145	0.4586	-0.1246	0.2681	0.2017	0.3737	-0.1798	-2.1358	0.2215	0.3531	-0.1547	0.0246	0.5303	0.0342	0.4028	-29.5306	13.7081	1.1512
13	5.6795	-0.3417	-1.8472	1.8756	-0.8207	2.5975	-0.3875	-0.0801	-1.3668	0.5108	0.0333	0.6394	0.3902	-1.6844	0.475	0.7326	-0.3936	0.3888	2.3248	-0.0376	0.5881	-43.7787	7.752	13.618
14	2.6218	0.817	-0.39	4.6022	-0.0811	3.5048	0.5905	-0.7927	-0.4876	0.8997	0.0252	0.5341	0.6186	-1.8148	0.1422	0.9287	-0.2599	0.1418	1.2021	0.0964	0.636	-37.682	7.1231	18.9966
15	3.977	-2.094	-0.2945	2.4337	0.2674	3.9923	-0.2623	0.2726	-0.8874	0.2032	0.0694	0.3928	0.969	-2.0383	0.1862	0.5821	-0.3742	0.0756	0.8329	-0.0091	0.5174	-31.8164	5.7143	2.4244
16	3.3861	0.8509	1.8765	2.7253	1.3096	4.5064	-0.2712	0.6248	-0.8531	-0.4007	-0.0996	1.0661	0.878	-2.2076	0.1249	0.5737	-0.4611	0.1218	1.3922	-0.0656	0.7109	-37.7807	5.3098	0.978
17	4.6203	-3.9895	-1.0042	5.1751	0.9112	6.4689	-0.6658	-0.6661	0.1842	1.0397	0.5751	-0.4806	1.0084	0.6104	0.0863	0.7086	0.0914	-0.105	0.3858	0.0345	0.3921	-13.9153	5.5113	13.2156

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 71:82)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 83:98)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 99:125)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 126:142)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 143:157)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 158:189)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 190:250)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 251:266)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 267:290)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 71:82)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 83:98)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 99:142)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 143:157)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 158:189)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 190:250)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 251:266)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 267:290)

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