PDB-8uan: The crystal structure of cobalt-bound human ADO C18S C239S varian...

ID or keywords:

Entry

Database: PDB / ID: 8uan

Title

The crystal structure of cobalt-bound human ADO C18S C239S variant at 1.99 Angstrom

Components

2-aminoethanethiol dioxygenase

Keywords

OXIDOREDUCTASE / cysteamine dioxygenase / cobalt-bound human ADO

Function / homology

Function and homology information

cysteamine dioxygenase / cysteamine dioxygenase activity / Degradation of cysteine and homocysteine / cellular response to hypoxia / iron ion binding / mitochondrion / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

Authors

Liu, A. / Li, J. / Duan, R. / Shin, I.

Funding support

United States, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2024
Title: Cobalt(II)-Substituted Cysteamine Dioxygenase Oxygenation Proceeds through a Cobalt(III)-Superoxo Complex.
Authors: Li, J. / Duan, R. / Liu, A.

History

Deposition	Sep 21, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8uan.cif.gz	66.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8uan.ent.gz	45.3 KB	Display	PDB format
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Validation report

Summary document	8uan_validation.pdf.gz	400.6 KB	Display	wwPDB validaton report
Full document	8uan_full_validation.pdf.gz	401.3 KB	Display
Data in XML	8uan_validation.xml.gz	6.9 KB	Display
Data in CIF	8uan_validation.cif.gz	10.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ua/8uan ftp://data.pdbj.org/pub/pdb/validation_reports/ua/8uan	HTTPS FTP

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Related structure data

Related structure data	8u9jC C: citing same article (ref.)
Similar structure data	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	#104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: 2-aminoethanethiol dioxygenase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	54.863, 95.920, 118.162
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	2-aminoethanethiol dioxygenase / Cysteamine dioxygenase Mass: 30108.080 Da / Num. of mol.: 1 / Mutation: C18S, C239S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADO / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SZ5
#2: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.56 Å³/Da / Density % sol: 52 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M (NH4)2SO4, 0.1 M Bis-Tris pH 5.5, 20% w/v PEG 3350

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL9-2	1	0.97946
SYNCHROTRON	SSRL	BL9-2	2	1.60471

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 6M	1	PIXEL	Dec 7, 2022
DECTRIS PILATUS 6M	2	PIXEL	Dec 7, 2022

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97946	1
2	1.60471	1

Reflection

Entry-ID: 8UAN

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	CC_1/2	CC star	R_merge(I) obs	R_pim(I) all	R_rim(I) all	Χ²	Diffraction-ID	Net I/σ(I)
1.99-50	21821	99.7	6.5	0.96	0.99	0.163	0.069	0.177	4.603	1	8.2
2.43-50	11974	99.6	21	0.9	0.973	0.336	0.07	0.344	0.963	2	4.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	Diffraction-ID	% possible all
1.99-2.02	6.1	0.487	1061	0.916	0.978	0.208	0.531	0.818	1	98
2.43-2.47	8.8	1.579	560	0.379	0.741	0.536	1.678	0.728	2	97.2
2.02-2.06	6.3	0.451	1069	0.938	0.984	0.192	0.491	0.885	1	100
2.47-2.52	9.8	1.837	590	0.412	0.764	0.576	1.934	0.706	2	98.7
2.06-2.1	6.4	0.42	1082	0.946	0.986	0.176	0.456	1.18	1	99.6
2.52-2.57	11	1.681	601	0.741	0.923	0.503	1.759	0.746	2	99.7
2.1-2.14	6.6	0.368	1071	0.962	0.99	0.155	0.4	1.012	1	100
2.57-2.62	13.3	2.052	583	0.817	0.948	0.567	2.131	0.709	2	99.5
2.14-2.19	6.6	0.35	1064	0.935	0.983	0.147	0.38	1.188	1	100
2.62-2.67	16.1	2.122	565	0.884	0.969	0.53	2.189	0.706		100
2.19-2.24	6.5	0.328	1085	0.952	0.988	0.138	0.357	1.364	1	99.8
2.67-2.74	17.9	2.828	616	0.886	0.969	0.659	2.906	0.71	2	100
2.24-2.3	6.2	0.303	1080	0.922	0.98	0.134	0.332	1.601	1	99.4
2.74-2.81	20.4	2.403	577	0.935	0.983	0.53	2.462	0.739	2	100
2.3-2.36	6.5	0.273	1059	0.949	0.987	0.116	0.298	1.821	1	100
2.81-2.88	22.7	2.085	623	0.964	0.991	0.438	2.131	0.753	2	99.8
2.36-2.43	6.8	0.256	1100	0.941	0.985	0.106	0.277	2.002	1	100
2.88-2.97	24.4	1.548	574	0.975	0.994	0.316	1.581	0.772		100
2.43-2.51	6.8	0.238	1082	0.948	0.986	0.099	0.258	2.455	1	99.7
2.97-3.06	24.1	1.446	596	0.949	0.987	0.295	1.476	0.815	2	100
2.51-2.6	6.7	0.222	1081	0.958	0.989	0.094	0.242	2.865	1	100
3.06-3.17	23.3	1.068	589	0.961	0.99	0.223	1.092	0.863	2	99.2
2.6-2.7	6.6	0.215	1077	0.952	0.988	0.09	0.234	3.539	1	99.8
3.17-3.3	23.7	0.768	587	0.975	0.994	0.16	0.785	0.881	2	100
2.7-2.82	6.1	0.207	1089	0.968	0.992	0.092	0.227	4.53	1	99.5
3.3-3.45	26.5	0.514	608	0.98	0.995	0.101	0.524	0.932	2	99.8
2.82-2.97	6.8	0.194	1089	0.946	0.986	0.081	0.21	5.391	1	100
3.45-3.63	26.5	0.384	591	0.975	0.994	0.077	0.392	0.966	2	99.8
2.97-3.16	6.8	0.185	1087	0.967	0.992	0.077	0.201	6.654	1	99.9
3.63-3.86	26.1	0.323	598	0.986	0.996	0.065	0.329	1.047	2	99.8
3.16-3.4	6.7	0.174	1109	0.966	0.991	0.072	0.189	8.055	1	100
3.86-4.15	25.4	0.226	601	0.989	0.997	0.053	0.272	1.08	2	100
3.4-3.74	6.2	0.163	1105	0.961	0.99	0.071	0.178	10.047	1	99.6
4.15-4.57	23	0.233	616	0.987	0.997	0.049	0.238	1.187	2	99.8
3.74-4.29	6.8	0.155	1112	0.969	0.992	0.066	0.169	11.482	1	100
4.57-5.23	25.9	0.23	613	0.99	0.998	0.045	0.234	1.185	2	100
4.29-5.4	6.4	0.149	1128	0.975	0.994	0.064	0.163	11.967	1	99.4
5.23-6.59	25.8	0.227	625	0.98	0.995	0.046	0.232	1.206	2	100
5.4-50	6.2	0.135	1191	0.984	0.996	0.059	0.148	11.46	1	99.7
6.59-50	23.3	0.269	661	0.995	0.988	0.056	0.276	1.636	2	99

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
SCALEPACK		data scaling
DENZO		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→47.62 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2354	1990	9.16 %
R_work	0.1981	-	-
obs	0.2015	21723	98.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.99→47.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1888	0	25	80	1993

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1962
X-RAY DIFFRACTION	f_angle_d	0.989	2665
X-RAY DIFFRACTION	f_dihedral_angle_d	19.708	270
X-RAY DIFFRACTION	f_chiral_restr	0.057	279
X-RAY DIFFRACTION	f_plane_restr	0.011	358

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 (%)
1.99-2.03	0.3242	135	0.3013	1286	X-RAY DIFFRACTION	91
2.03-2.09	0.2845	130	0.2592	1384	X-RAY DIFFRACTION	99
2.09-2.15	0.2612	138	0.2413	1395	X-RAY DIFFRACTION	99
2.15-2.22	0.3228	143	0.2292	1400	X-RAY DIFFRACTION	100
2.22-2.3	0.2846	146	0.2361	1395	X-RAY DIFFRACTION	99
2.3-2.39	0.2534	136	0.228	1402	X-RAY DIFFRACTION	100
2.39-2.5	0.2833	136	0.2178	1427	X-RAY DIFFRACTION	100
2.5-2.63	0.2666	146	0.2246	1388	X-RAY DIFFRACTION	100
2.63-2.8	0.2537	139	0.2279	1411	X-RAY DIFFRACTION	100
2.8-3.01	0.2565	147	0.2195	1404	X-RAY DIFFRACTION	100
3.01-3.32	0.2532	144	0.2178	1435	X-RAY DIFFRACTION	100
3.32-3.8	0.2344	147	0.1898	1431	X-RAY DIFFRACTION	100
3.8-4.78	0.2002	150	0.1595	1450	X-RAY DIFFRACTION	100
4.78-47.62	0.2005	153	0.1771	1525	X-RAY DIFFRACTION	100

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