PDB-7lvz: Crystal structure of ADO

ID or keywords:

Entry

Database: PDB / ID: 7lvz

Title

Crystal structure of ADO

Components

2-aminoethanethiol dioxygenase

Keywords

OXIDOREDUCTASE / CUPIN DIOXYGENASE cysteine oxidation non-heme Iron enzyme

Function / homology

Function and homology information

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

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

Bingman, C.A. / Fernandez, R.L. / Smith, R.W. / Fox, B.G. / Brunold, T.C.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	1R01GM117120-01A1	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	T32GM008505	United States

Citation

Journal: Biochemistry / Year: 2021
Title: The Crystal Structure of Cysteamine Dioxygenase Reveals the Origin of the Large Substrate Scope of This Vital Mammalian Enzyme.
Authors: Fernandez, R.L. / Elmendorf, L.D. / Smith, R.W. / Bingman, C.A. / Fox, B.G. / Brunold, T.C.

History

Deposition	Feb 26, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 5, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Refinement description / Category: chem_comp_atom / chem_comp_bond / software / Item: _software.name
Revision 1.2	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7lvz.cif.gz	692.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7lvz.ent.gz	480.3 KB	Display	PDB format
PDBx/mmJSON format	7lvz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7lvz_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	7lvz_full_validation.pdf.gz	2.1 MB	Display
Data in XML	7lvz_validation.xml.gz	39.8 KB	Display
Data in CIF	7lvz_validation.cif.gz	58.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lv/7lvz ftp://data.pdbj.org/pub/pdb/validation_reports/lv/7lvz	HTTPS FTP

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Related structure data

Similar structure data	5r3w-d 5r2k-d 5p4w-d 5oyv-d 5r26-d 5r2w-d 5lpw-d 3svv-2 3gqm-1 3fzt-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

Deposited unit

A: 2-aminoethanethiol dioxygenase

B: 2-aminoethanethiol dioxygenase

C: 2-aminoethanethiol dioxygenase

D: 2-aminoethanethiol dioxygenase

hetero molecules

114 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-aminoethanethiol dioxygenase

hetero molecules

defined by author&software
28.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 2-aminoethanethiol dioxygenase

hetero molecules

defined by author&software
28.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 2-aminoethanethiol dioxygenase

hetero molecules

defined by author&software
28.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: 2-aminoethanethiol dioxygenase

hetero molecules

defined by author&software
28.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	54.296, 139.525, 142.007
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	2-aminoethanethiol dioxygenase / Cysteamine dioxygenase Mass: 28406.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ado, Gm237 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6PDY2, cysteamine dioxygenase
#2: Chemical	ChemComp-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.5 Å³/Da / Density % sol: 50.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Crystals were grown in a Coy anaerobic chamber.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12706 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 27, 2020
Radiation	Monochromator: Silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.12706 Å / Relative weight: 1
Reflection	Resolution: 1.89→39.17 Å / Num. obs: 86883 / % possible obs: 87.21 % / Redundancy: 13.2 % / B_iso Wilson estimate: 34.34 Å² / CC_1/2: 0.994 / CC star: 0.998 / R_merge(I) obs: 0.1844 / R_pim(I) all: 0.05248 / R_rim(I) all: 0.1919 / Net I/σ(I): 12.34
Reflection shell	Resolution: 1.89→1.958 Å / Redundancy: 12.6 % / R_merge(I) obs: 1.657 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 4059 / CC_1/2: 0.474 / CC star: 0.802 / R_pim(I) all: 0.4784 / R_rim(I) all: 1.726 / % possible all: 47.39

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
PHASER	1.19_4092	phasing
autoPROC	1.0.5 (20200520)	data reduction
XDS	Jan 31, 2020 (BUILT 20200417)	data scaling
Aimless	0.7.4	data processing
STARANISO	2.3.36 (20200511)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ussA iTasser homology model residues 83-133, 170-209

Resolution: 1.89→39.17 Å / SU ML: 0.2295 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5115
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2276	2519	3.31 %
R_work	0.1913	73557	-
obs	0.1925	76076	87.22 %

Solvent computation

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

Displacement parameters

B_iso mean: 46.47 Å²

Refinement step

Cycle: LAST / Resolution: 1.89→39.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7557	0	10	554	8121

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0098	7828
X-RAY DIFFRACTION	f_angle_d	0.8677	10699
X-RAY DIFFRACTION	f_chiral_restr	0.051	1147
X-RAY DIFFRACTION	f_plane_restr	0.0091	1445
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9883	3023

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 (%)
1.89-1.93	0.3309	75	0.2816	1869	X-RAY DIFFRACTION	40.75
1.93-1.97	0.3003	86	0.2651	2623	X-RAY DIFFRACTION	56.72
1.97-2.01	0.317	94	0.2573	3089	X-RAY DIFFRACTION	66.19
2.01-2.06	0.2633	108	0.2506	3308	X-RAY DIFFRACTION	71.98
2.06-2.11	0.2607	129	0.2397	3575	X-RAY DIFFRACTION	77.04
2.11-2.16	0.2791	133	0.2396	3802	X-RAY DIFFRACTION	82.24
2.16-2.23	0.2777	137	0.2272	3971	X-RAY DIFFRACTION	85.82
2.23-2.3	0.2717	165	0.2261	4287	X-RAY DIFFRACTION	92.58
2.3-2.38	0.2505	163	0.2094	4568	X-RAY DIFFRACTION	97.97
2.38-2.48	0.2279	152	0.2016	4643	X-RAY DIFFRACTION	99.77
2.48-2.59	0.2421	141	0.2074	4702	X-RAY DIFFRACTION	99.86
2.59-2.73	0.2223	141	0.2042	4669	X-RAY DIFFRACTION	99.75
2.73-2.9	0.2695	142	0.2208	4680	X-RAY DIFFRACTION	99.77
2.9-3.12	0.2545	142	0.2005	4719	X-RAY DIFFRACTION	100
3.12-3.43	0.2215	191	0.1944	4695	X-RAY DIFFRACTION	99.98
3.43-3.93	0.2123	236	0.1701	4664	X-RAY DIFFRACTION	99.96
3.93-4.95	0.1705	144	0.1467	4684	X-RAY DIFFRACTION	97.22
4.95-39.17	0.2308	140	0.1807	5009	X-RAY DIFFRACTION	99.65

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	1.99503607822	-1.29152113636	0.864740494983	1.18336346861	-0.193896469957	2.48097924187	-0.0816674041937	-0.0923938180429	0.242415878601	0.208069009666	-0.160934376723	0.370117542387	0.22765162213	-0.249327204441	-0.00140481603639	0.43076444519	-0.0343918773913	0.119677873487	0.485735233768	0.0299967839739	0.412274765083	21.0912339177	45.3839790428	42.709719354
2	0.935954075163	0.122689410933	0.563938260986	0.668091845262	-0.170101271897	0.586963347117	0.0662315445174	0.362114409385	-0.574371165926	-0.194731383388	-0.0559019749055	-0.758218324353	0.354183548049	0.688702415018	9.56382741641E-7	0.364169347786	0.0775056390566	0.0119438219235	0.456554962187	-0.0365680419708	0.504892235073	55.1755921613	77.608233677	59.2892165728
3	1.48366920517	1.29690328985	0.555817196113	2.05438039935	-0.430361310355	2.54772573143	-0.115327687655	0.224819424331	0.168330893423	-0.123570150596	-0.0438680853939	0.117447301401	-0.251415266652	-0.120941472119	-0.00673877275009	0.279805269703	0.0620709476858	-0.0393946106939	0.273993326948	-0.029443349797	0.240310666862	38.108437597	87.8677973487	53.3053606923
4	0.88586862163	0.907310933241	-0.213755040548	3.14383750737	0.999995599725	1.47256478858	0.0293953979923	0.0947145105341	-0.199154210209	-0.00167301482819	-0.171400376081	0.286101182818	0.114203721996	-0.205724750084	-0.000462995372442	0.299025300709	0.0536206669809	-0.0312138609847	0.31194137764	-0.0467856299982	0.356275330364	31.6818708316	72.1719868728	56.5473902771
5	1.46955843033	0.141195902411	1.21058679774	1.93481023851	0.76320920473	1.86070363041	-0.140448991571	0.2334679931	-0.219541249161	-0.0645227982522	-0.0108187632745	0.298912021856	0.138831240247	-0.232779962852	-0.00412725083131	0.31527607163	0.0637776661921	0.0243546364148	0.308906531047	-0.0814830842156	0.362683636646	30.4631758781	76.0544549195	52.8864192902
6	1.51068093735	0.0345991019659	0.844958903235	1.87278638279	0.549902131843	2.08042766948	0.0171171143635	-0.0819805953712	-0.217153216944	-0.281341330324	-0.0325526619796	0.228626459485	0.0847827625132	-0.323684131889	-0.00439733419185	0.221573176255	0.00335721812013	-0.0373355766447	0.25723901767	0.00546269260398	0.326585750634	-2.53967988503	86.5764225144	79.4354442176
7	1.58745913982	-1.54831699716	-0.0731288302705	2.63099388715	0.231594393113	0.82483714273	0.0544956804696	-0.0300146864781	-0.0726525562137	-0.241675678393	-0.0880232352209	-0.273246738441	-0.0289318084682	0.137314294174	-0.0014276459946	0.233448553805	-0.0357750261645	0.0233733435035	0.235660084402	0.0307004307052	0.287594755106	17.0253716995	83.3431142687	82.6497878652
8	1.56778761451	-0.447421292742	0.9335739844	2.22439788228	-0.0452013390818	0.881853334508	0.040039130265	-0.296072129197	-0.0966051157691	-0.0565107885546	0.0785074884027	-0.311109573183	0.0347946798065	0.184607985558	3.35516277973E-5	0.274218186598	-0.0624458713246	-0.000711274973743	0.309047932047	0.046556727732	0.367724702352	19.4935334321	83.7908169029	85.608904195
9	0.666573309666	0.240246896609	0.0593715625122	0.776641645727	-0.167304999041	0.537963809763	-0.0917422387673	-0.444211118286	0.0795814967233	0.19685986022	0.0960855801059	0.676473428183	0.221630880368	-0.541493863775	-7.83372752614E-5	0.40665275262	-0.0606695387682	0.0509051596353	0.573304931349	0.0720462966823	0.429997405896	12.2502956045	48.383372981	97.2998066688
10	2.44297984291	0.884346639445	0.94018018186	3.28432182078	-0.103316346477	2.12393809026	-0.204917492677	0.226293202078	-0.0928627648197	-0.39758679396	0.239864392357	-0.159386031632	0.218216362074	0.0817198917429	0.00244633610837	0.307459455215	-0.0248043055994	0.0423502946629	0.259260584917	0.00274246196614	0.260408278297	27.7732938086	52.5310131871	86.2185209568
11	0.260418030831	0.226043830664	0.212037680028	0.653108358345	0.259862465631	0.49635099254	-0.0173177425419	0.481620887419	-0.365128546984	-0.364089878759	0.0195960635218	-0.140391917263	-0.0483087020473	0.347784783436	0.000164845202279	0.405637264917	0.0555472729134	0.0217157320774	0.614140324719	-0.0577962366291	0.303057892408	50.1632023712	56.5055078982	109.330076884
12	0.47584786576	-0.0870246571098	0.238036689906	0.114214019301	-0.173828130677	0.463956675194	0.0558473594442	-0.188202593433	-0.11559646446	-0.256421498567	0.0559487024064	-0.351161508585	0.0163999589632	0.206153626561	1.08037475398E-5	0.566246141446	0.0256701292857	-0.0199804375302	0.545427311842	0.0082422598815	0.462860417941	42.6255116923	52.4979468124	102.250985456
13	0.292936452086	0.106466761047	-0.126807392295	0.482597409937	-0.198092612661	0.101324813025	0.0619987468737	-0.411850995913	-0.747163890723	0.628633291959	0.256043798301	-0.0617891811837	1.13045846141	-0.0809792029938	-0.00440092810575	0.455747266031	0.0271158532259	-0.0184744979175	0.360591607936	0.0260987433557	0.414412433682	26.8026247666	45.7915254422	97.9308554632
14	2.08241493528	1.21134748365	0.877245071739	1.66615365152	-0.331854445672	3.31225902476	-0.0543198896834	0.00112129736465	0.358874773172	0.0175201892222	0.011095619423	-0.263566444055	0.0454563087276	0.252637325765	0.000615358824507	0.325473877597	0.0111948720381	0.0342433853577	0.317523311942	-0.0469076015151	0.342553954837	34.0002872249	55.0694246075	93.5734591129
15	1.27124285945	0.131573096652	1.2037146197	1.93953463908	1.11676620064	1.71324797483	-0.294121910915	-0.100499390723	0.368934409311	0.649271797325	0.405903700042	-0.41173319247	0.810756103038	0.867638137273	0.0041536415498	0.660499087569	0.179025182983	0.0142862475745	0.525267075834	0.0355588686634	0.434006585595	40.9305019698	42.0025532061	50.640819369
16	1.90287669297	0.169717438211	2.34257825176	1.54997900974	0.851462351153	3.73018751717	0.178263542927	-0.218452833973	0.00384047144954	0.505962492702	-0.0656994809399	0.209325153556	0.566789047846	-0.347198755037	0.00532053819891	0.4667441132	-0.0569513224049	0.106925131505	0.341757353579	-0.00773294419007	0.282686124398	23.1112553406	43.4330778941	43.4864985427

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'D' and (resid 196 through 256 )	D	J	196 - 256	186 - 246
2	2	chain 'A' and (resid 7 through 48 )	A	A	7 - 48	1 - 34
3	3	chain 'A' and (resid 49 through 105 )	A	A	49 - 105	35 - 91
4	4	chain 'A' and (resid 106 through 202 )	A	A	106 - 202	92 - 188
5	5	chain 'A' and (resid 203 through 256 )	A	A	203 - 256	189 - 236
6	6	chain 'B' and (resid 5 through 64 )	B	D	5 - 64	1 - 53
7	7	chain 'B' and (resid 65 through 195 )	B	D	65 - 195	54 - 184
8	8	chain 'B' and (resid 196 through 256 )	B	D	196 - 256	185 - 245
9	9	chain 'C' and (resid 7 through 48 )	C	G	7 - 48	1 - 34
10	10	chain 'C' and (resid 49 through 123 )	C	G	49 - 123	35 - 109
11	11	chain 'C' and (resid 124 through 144 )	C	G	124 - 144	110 - 130
12	12	chain 'C' and (resid 145 through 162 )	C	G	145 - 162	131 - 148
13	13	chain 'C' and (resid 163 through 177 )	C	G	163 - 177	149 - 163
14	14	chain 'C' and (resid 178 through 256 )	C	G	178 - 256	164 - 238
15	15	chain 'D' and (resid 7 through 64 )	D	J	7 - 64	1 - 54
16	16	chain 'D' and (resid 65 through 195 )	D	J	65 - 195	55 - 185

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi