PDB-8z1i: Crystal structure of the isomerase Art22 with ethylene glycol

ID or keywords:

Entry

Database: PDB / ID: 8z1i

Title

Crystal structure of the isomerase Art22 with ethylene glycol

Components

Art22

Keywords

ISOMERASE / isomerization / oxygenation / cleavage of ketohexose

Function / homology

:

Function and homology information

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Guo, L. / Li, P.W. / Li, D.F. / Chen, Y.H.

Funding support

China, 2items

Citation

Journal: Nat Catal / Year: 2025
Title: Oxidative cleavage of hexopyranose by a TIM-barrel isomerase
Authors: Li, P. / Wang, D. / Guo, L. / Chen, Y. / Mao, H. / Zhao, Z. / Wang, M. / Chen, M. / Xu, Z. / Wang, B. / Li, D. / Chen, Y.

History

Deposition	Apr 11, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 16, 2025	Provider: repository / Type: Initial release
Revision 1.1	Oct 22, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8z1i.cif.gz	322.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8z1i.ent.gz	269 KB	Display	PDB format
PDBx/mmJSON format	8z1i.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8z1i_validation.pdf.gz	458.2 KB	Display	wwPDB validaton report
Full document	8z1i_full_validation.pdf.gz	461.1 KB	Display
Data in XML	8z1i_validation.xml.gz	30.6 KB	Display
Data in CIF	8z1i_validation.cif.gz	42.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z1/8z1i ftp://data.pdbj.org/pub/pdb/validation_reports/z1/8z1i	HTTPS FTP

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Related structure data

Related structure data	9kojC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Art22

B: Art22

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	46.276, 77.627, 149.476
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Art22 Mass: 33527.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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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 Å³/Da / Density % sol: 38.56 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.03M Citric acid, 0.07M BIS-TRIS propane, 20% w/v Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979191 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979191 Å / Relative weight: 1
Reflection	Resolution: 1.45→53.9 Å / Num. obs: 94556 / % possible obs: 98.16 % / Redundancy: 13 % / CC_1/2: 0.999 / R_merge(I) obs: 0.05295 / R_pim(I) all: 0.01563 / R_rim(I) all: 0.0553 / Net I/σ(I): 24.43
Reflection shell	Resolution: 1.45→1.502 Å / R_merge(I) obs: 0.7532 / Mean I/σ(I) obs: 3.15 / Num. unique obs: 9193 / CC_1/2: 0.915 / R_rim(I) all: 0.787

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→53.84 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1922	2000	2.12 %	RANDOM
R_work	0.1691	-	-	-
obs	0.1696	94539	98.16 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.45→53.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4318	0	32	503	4853

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4409
X-RAY DIFFRACTION	f_angle_d	1.148	5943
X-RAY DIFFRACTION	f_dihedral_angle_d	3.989	1663
X-RAY DIFFRACTION	f_chiral_restr	0.088	671
X-RAY DIFFRACTION	f_plane_restr	0.007	762

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 (%)
1.45-1.4863	0.3244	139	0.2864	6408	X-RAY DIFFRACTION	96
1.4863-1.5265	0.2852	139	0.247	6440	X-RAY DIFFRACTION	97
1.5265-1.5714	0.2941	139	0.2287	6433	X-RAY DIFFRACTION	97
1.5714-1.6221	0.2168	140	0.2056	6504	X-RAY DIFFRACTION	98
1.6221-1.6801	0.2407	141	0.1967	6520	X-RAY DIFFRACTION	98
1.6801-1.7473	0.1957	142	0.188	6522	X-RAY DIFFRACTION	98
1.7473-1.8269	0.2088	141	0.1846	6546	X-RAY DIFFRACTION	98
1.8269-1.9232	0.2128	142	0.1804	6581	X-RAY DIFFRACTION	98
1.9232-2.0437	0.1829	143	0.1651	6616	X-RAY DIFFRACTION	99
2.0437-2.2015	0.1916	143	0.1575	6649	X-RAY DIFFRACTION	99
2.2015-2.423	0.2016	145	0.1618	6706	X-RAY DIFFRACTION	99
2.423-2.7736	0.1604	145	0.1647	6723	X-RAY DIFFRACTION	99
2.7736-3.4944	0.1759	149	0.1602	6821	X-RAY DIFFRACTION	100
3.4944-53.84	0.1848	152	0.1589	7070	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	0.302	0.0743	0.0273	0.5391	0.1368	0.4135	-0.0001	-0.0945	0.0113	-0.1207	-0.0517	0.0636	-0.0094	-0.0456	0	0.1629	0.0002	-0.0123	0.1553	-0.0105	0.182	14.8731	13.8782	96.3865
2	0.7151	-0.0218	0.3056	0.1114	0.0122	0.7909	0.0073	-0.0159	-0.0343	-0.0636	-0.0188	-0.0359	-0.0611	-0.1207	0.0001	0.1227	0.0034	0.0026	0.1292	-0.0031	0.1512	18.565	17.5292	105.8455
3	0.7958	0.1609	-0.1912	-0.197	-0.4947	0.5559	0.0361	-0.0238	0.0738	-0.0323	0.013	0.0144	-0.0695	-0.0551	-0	0.1755	-0.0015	0.021	0.145	-0.0005	0.1603	29.7081	25.3312	108.1802
4	0.8099	-0.2178	0.6513	0.4361	0.2206	0.5532	0.1031	-0.1627	0.0658	0.0129	-0.0976	-0.0424	-0.1024	0.3037	0.0001	0.1722	-0.017	0.011	0.1657	-0.0073	0.1616	40.0443	24.483	108.8429
5	1.1346	0.4293	-0.3182	0.616	-0.0175	0.4572	-0.0158	0.0473	-0.1575	-0.0821	0.0183	-0.0998	-0.0299	0.0366	-0	0.1692	0.0108	0.0103	0.1515	-0.0109	0.1657	39.1495	13.2742	99.7202
6	0.6829	0.1535	0.3683	0.0821	-0.3392	0.1039	-0.1467	0.2599	0.0331	0.0199	-0.0686	-0.151	0.1044	0.1931	0.0034	0.17	-0.0171	0.0141	0.2456	0.0197	0.1838	34.3811	11.6527	89.4558
7	1.0952	0.3342	-0.1818	0.2645	0.0656	0.2992	-0.0964	0.1371	-0.2625	0.0734	0.0708	0.0523	0.0227	0.0587	0	0.2021	0.0192	0.0005	0.1857	-0.0273	0.2096	28.1805	3.956	93.45
8	0.2896	0.2977	0.0596	0.2007	0.0108	0.0832	0.0229	0.122	-0.3232	-0.1697	0.0058	0.2077	0.0629	-0.0843	-0.0005	0.201	-0.0173	-0.0101	0.1881	-0.0576	0.2196	19.1775	2.679	89.3449
9	0.5244	0.1263	-0.5971	0.4218	0.0275	0.5967	-0.0529	-0.066	0.068	-0.0314	0.0505	-0.0448	0.0569	0.0955	0.0001	0.1834	0.0113	0.018	0.1955	-0.0061	0.1769	44.5902	39.7413	83.8288
10	0.475	-0.0758	-0.274	0.4751	0.3359	0.2586	0.0181	-0.0213	0.0219	0.0282	0.0509	-0.0514	0.0599	0.0708	0.0011	0.1455	0.0024	0.0029	0.1543	-0.0178	0.1515	40.9368	44.8909	92.6463
11	0.4191	0.0817	-0.204	0.4827	0.0766	-0.1513	0.0228	0.0025	-0.0187	0.0677	0.0291	0.0216	0.0387	0.0447	0.0001	0.1751	0.0018	0.0014	0.153	-0.0287	0.1747	29.7394	41.9787	100.0445
12	0.5537	-0.5538	-0.0354	0.4449	0.3263	0.3669	0.0796	-0.1551	0.0304	0.0439	-0.0989	0.1636	-0.0057	-0.0566	0	0.1816	0.002	0.0126	0.1749	-0.0193	0.1534	19.3665	42.9885	99.8034
13	0.7633	0.4972	0.3698	0.1153	0.1029	0.6349	0.0137	0.0845	-0.034	-0.0753	0.0156	-0.002	0.1185	-0.0278	-0	0.1928	0.0115	0.0099	0.1759	-0.0285	0.1651	20.7086	42.0205	86.9866
14	1.0559	-0.1045	-0.2711	0.2156	0.2951	-0.0186	0.0058	0.1907	-0.193	-0.0208	-0.0071	0.1198	-0.125	-0.0168	0.0007	0.1614	0.0076	-0.0068	0.2027	-0.0306	0.2184	22.7349	39.6341	77.9193
15	1.432	0.0904	-0.3312	0.083	0.06	0.5677	-0.129	0.3549	-0.013	0.1035	0.0273	0.0702	-0.0617	-0.1634	-0.0021	0.1739	0.0189	-0.008	0.2532	-0.0002	0.1529	31.2648	42.4264	74.1484
16	0.3861	0.3976	-0.2965	0.6628	-0.0445	0.3878	0.018	0.4768	0.0572	-0.1676	-0.0397	-0.1477	0.1019	0.1904	0.0129	0.1982	-0.0066	0.0277	0.3303	-0.0076	0.1404	39.2091	42.6661	69.6406

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 30 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 74 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 75 through 112 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 113 through 137 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 138 through 192 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 193 through 224 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 225 through 258 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 259 through 274 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 30 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 31 through 74 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 75 through 112 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 113 through 137 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 138 through 184 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 185 through 221 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 222 through 258 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 259 through 277 )

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