PDB-9koj: Crystal structure of the isomerase Art22

ID or keywords:

Entry

Database: PDB / ID: 9koj

Title

Crystal structure of the isomerase Art22

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: 1.445 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	Nov 20, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 30, 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	9koj.cif.gz	233.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9koj.ent.gz	187.1 KB	Display	PDB format
PDBx/mmJSON format	9koj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/9koj ftp://data.pdbj.org/pub/pdb/validation_reports/ko/9koj	HTTPS FTP

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Related structure data

Related structure data	8z1iC 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

67.5 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)	46.460, 78.005, 150.398
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-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 397 / 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: BL18U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 1.445→37.6 Å / Num. obs: 98532 / % possible obs: 99.76 % / Redundancy: 12.8 % / CC_1/2: 0.997 / R_merge(I) obs: 0.1118 / R_pim(I) all: 0.03249 / R_rim(I) all: 0.1165 / Net I/σ(I): 12.58
Reflection shell	Resolution: 1.445→1.496 Å / R_merge(I) obs: 0.6986 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 9571 / CC_1/2: 0.927 / R_rim(I) all: 0.728

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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: 1.445→37.599 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2029	1998	2.03 %	RANDOM
R_work	0.1782	-	-	-
obs	0.1787	98510	99.73 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.445→37.599 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4374	0	17	397	4788

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4461
X-RAY DIFFRACTION	f_angle_d	0.941	6020
X-RAY DIFFRACTION	f_dihedral_angle_d	3.769	1686
X-RAY DIFFRACTION	f_chiral_restr	0.079	684
X-RAY DIFFRACTION	f_plane_restr	0.006	777

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 (%)
1.445-1.4808	0.2762	135	0.2539	6558	X-RAY DIFFRACTION	96
1.4808-1.5209	0.2377	140	0.2141	6825	X-RAY DIFFRACTION	100
1.5209-1.5656	0.2112	142	0.1998	6827	X-RAY DIFFRACTION	100
1.5656-1.6161	0.222	141	0.1875	6850	X-RAY DIFFRACTION	100
1.6161-1.6739	0.1897	142	0.1777	6819	X-RAY DIFFRACTION	100
1.6739-1.7409	0.2214	143	0.1815	6853	X-RAY DIFFRACTION	100
1.7409-1.8202	0.2097	141	0.1823	6870	X-RAY DIFFRACTION	100
1.8202-1.9161	0.2509	143	0.193	6866	X-RAY DIFFRACTION	100
1.9161-2.0362	0.2175	143	0.1812	6897	X-RAY DIFFRACTION	100
2.0362-2.1933	0.1901	143	0.1718	6905	X-RAY DIFFRACTION	100
2.1933-2.414	0.1878	144	0.1778	6928	X-RAY DIFFRACTION	100
2.414-2.7633	0.2205	144	0.1826	6988	X-RAY DIFFRACTION	100
2.7633-3.481	0.2161	146	0.1804	7022	X-RAY DIFFRACTION	100
3.481-37.599	0.1704	151	0.1613	7304	X-RAY DIFFRACTION	100

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	0.434	-0.0222	-0.5068	0.2619	-0.0885	0.554	-0.0107	0.0392	0.0239	0.0884	0.0296	0.018	0.0734	-0.0742	0	0.1495	-0.0129	0.0039	0.1564	-0.0043	0.1495	1.6282	0.7857	-9.3422
2	0.5663	0.2269	-0.2082	0.494	-0.2024	0.1355	0.0211	-0.0003	0.0471	-0.0393	0.0523	0.0666	0.0469	-0.0418	0.002	0.1503	0.0074	-0.0043	0.1456	0.0093	0.14	5.341	5.7452	-18.2357
3	0.2705	0.1166	-0.0724	0.4141	-0.1035	0.1839	-0.0126	0.026	0.0055	-0.0897	0.0539	0.024	-0.0067	-0.0359	-0	0.1378	-0.005	0.0025	0.122	0.0185	0.136	16.5103	2.7475	-25.6322
4	0.5508	0.5488	-0.1377	0.4835	-0.0982	0.1391	0.019	0.1438	0.0405	-0.0319	-0.057	-0.1731	-0.026	0.0408	-0.0001	0.1518	-0.0005	0.0113	0.1582	0.0189	0.117	26.9103	3.7753	-25.4607
5	0.4967	-0.3581	0.2219	0.2174	0.089	0.6814	0.0332	-0.0702	0.0186	0.0333	0.0059	0.0149	0.054	0.012	-0	0.1528	-0.0137	0.0039	0.1406	0.0215	0.1346	25.6306	2.955	-12.6052
6	0.1269	-0.0486	-0.1475	0.3143	-0.0551	0.1385	0.0806	-0.1999	0.1128	0.011	-0.0316	-0.0254	0.0014	0.0916	-0	0.167	-0.0233	-0.0035	0.1931	-0.0145	0.1559	24.7375	8.9272	-5.395
7	0.1786	-0.0941	0.2344	0.181	-0.0166	1.1319	0.1165	-0.2361	-0.8051	0.0876	0.0025	-0.5906	0.0378	-0.0531	0.0388	0.1715	0.0095	-0.0408	0.2097	0.0685	0.5535	21.9204	-12.2575	-1.3747
8	1.5945	0.0746	-0.1816	0.4872	-0.1216	0.9777	0.0107	-0.3646	-0.0118	0.0576	-0.021	-0.0299	-0.091	0.1073	-0.0006	0.1495	-0.0236	0.0046	0.2273	-0.0207	0.1213	12.4112	3.5463	1.8462
9	0.2368	-0.2171	0.0445	0.2525	-0.1113	0.3251	-0.0196	0.0074	0.0197	0.0597	-0.002	-0.0275	0.0211	0.1172	0.0001	0.1485	0.0028	-0.0046	0.1319	-0.0007	0.1697	31.5872	-25.4753	-21.5827
10	0.7335	0.2422	0.0185	0.1762	-0.0867	0.9667	0.0443	0.0543	0.0072	0.037	-0.0685	-0.0054	-0.0928	0.1559	0.0003	0.1507	-0.0054	0.0064	0.1525	-0.0093	0.1548	27.7965	-21.94	-31.0489
11	0.46	-0.0584	-0.0487	-0.0016	0.3793	0.508	0.0155	0.0223	0.0505	-0.0176	0.0397	0.004	-0.068	0.087	0.0005	0.1507	-0.0013	0.0194	0.1413	-0.0116	0.1331	16.5505	-14.0432	-33.5416
12	0.9802	0.1842	-0.3991	0.7271	0.0365	0.4785	0.0392	0.037	-0.0585	0.0303	-0.037	0.0478	-0.0145	-0.0838	0.0001	0.1429	0.0085	-0.0053	0.1371	-0.0061	0.1256	7.0874	-20.9918	-28.5588
13	0.1242	-0.1918	-0.0025	0.2609	0.0138	0.2027	0.0356	-0.0163	-0.1868	0.0633	-0.0407	0.1707	0.0246	-0.0805	0.0001	0.1523	-0.0134	-0.014	0.1514	-0.0054	0.232	8.4966	-33.704	-25.3189
14	0.0206	-0.0236	0.0005	0.3006	-0.0483	0.2814	0.04	-0.4339	0.2354	-0.0102	-0.1843	0.2232	-0.045	-0.4214	-0.0045	0.1735	0.0173	0.0194	0.434	-0.042	0.2646	11.448	-23.5112	-6.6471
15	1.5199	0.0951	0.1501	0.7256	-0.3295	0.6931	-0.0317	-0.186	-0.3016	-0.0234	0.0493	0.0809	0.0815	0.021	0.013	0.1606	-0.006	-0.0097	0.1391	0.0289	0.2397	20.5926	-35.4728	-16.2239

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 30 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 31 through 74 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 75 through 112 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 113 through 137 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 138 through 184 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 185 through 201 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 202 through 220 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 221 through 278 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1 through 30 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 31 through 74 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 75 through 112 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 113 through 184 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 185 through 201 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 202 through 219 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 220 through 278 )

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