PDB-7vgk: Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-he...

ID or keywords:

Entry

Database: PDB / ID: 7vgk

Title

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI

Components

4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

Keywords

ISOMERASE / hexuronate-metabolizing enzyme / Lactobacillus / heparin

Function / homology

Function and homology information

5-dehydro-4-deoxy-D-glucuronate isomerase / 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity / pectin catabolic process / zinc ion binding
Similarity search - Function

Biological species

Lactobacillus rhamnosus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Iwase, H. / Oiki, S. / Mikami, B. / Takase, R. / Hashimoto, W.

Funding support

Japan, 1items

Citation

Journal: J.Appl.Glyosci. / Year: 2023
Title: Crystal structures of Lacticaseibacillus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI in complex with substrate analogs
Authors: Iwase, H. / Yamamoto, Y. / Yamada, A. / Kawai, K. / Oiki, S. / Watanabe, D. / Mikami, B. / Takase, R. / Hashimoto, W.

History

Deposition	Sep 16, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 19, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.2	Nov 29, 2023	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7vgk_validation.pdf.gz	470.8 KB	Display	wwPDB validaton report
Full document	7vgk_full_validation.pdf.gz	485.1 KB	Display
Data in XML	7vgk_validation.xml.gz	51.1 KB	Display
Data in CIF	7vgk_validation.cif.gz	67.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vg/7vgk ftp://data.pdbj.org/pub/pdb/validation_reports/vg/7vgk	HTTPS FTP

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Related structure data

Related structure data	7e4sC 1ywkS S: Starting model for refinement 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

Deposited unit

A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

C: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

D: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

E: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

F: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

183 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

E: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

defined by author&software
Evidence: gel filtration
60.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

F: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

defined by author&software
60.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

D: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

defined by author&software
60.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.190, 130.980, 157.315
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase / 5-keto-4-deoxyuronate isomerase / DKI isomerase Mass: 30445.465 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Gene: kduI, kduI1, GKD16_00900, LRHP540_00845 / Production host: Escherichia coli B (bacteria) References: UniProt: A0A508YKK7, 5-dehydro-4-deoxy-D-glucuronate isomerase

#1: Protein

4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase / 5-keto-4-deoxyuronate isomerase / DKI isomerase

Mass: 30445.465 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Lactobacillus rhamnosus (bacteria) / Gene: kduI, kduI1, GKD16_00900, LRHP540_00845 / Production host:

Escherichia coli B (bacteria)
References: UniProt: A0A508YKK7, 5-dehydro-4-deoxy-D-glucuronate isomerase

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: PEG 8000, magnesium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 8, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. obs: 35643 / % possible obs: 99.4 % / Redundancy: 5.7 % / R_pim(I) all: 0.044 / R_rim(I) all: 0.098 / Net I/σ(I): 20.8
Reflection shell	Resolution: 3.1→3.15 Å / R_merge(I) obs: 0.596 / Num. unique obs: 1735 / CC_1/2: 0.614 / R_pim(I) all: 0.265

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Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
HKL2Map		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ywk

1ywk

Resolution: 3.1→45.12 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2384	1742	4.9 %
R_work	0.194	-	-
obs	0.1963	35554	99.18 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.1→45.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12377	0	0	0	12377

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	12707
X-RAY DIFFRACTION	f_angle_d	0.511	17204
X-RAY DIFFRACTION	f_dihedral_angle_d	20.648	4646
X-RAY DIFFRACTION	f_chiral_restr	0.043	1821
X-RAY DIFFRACTION	f_plane_restr	0.003	2226

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 (%)
3.1-3.2	0.3717	137	0.2876	2696	X-RAY DIFFRACTION	97
3.2-3.3	0.2947	164	0.2737	2759	X-RAY DIFFRACTION	100
3.3-3.42	0.3222	134	0.2504	2813	X-RAY DIFFRACTION	100
3.42-3.55	0.3065	141	0.2361	2797	X-RAY DIFFRACTION	100
3.55-3.72	0.2505	138	0.213	2815	X-RAY DIFFRACTION	100
3.72-3.91	0.2856	137	0.212	2826	X-RAY DIFFRACTION	100
3.91-4.16	0.2378	154	0.1909	2819	X-RAY DIFFRACTION	100
4.16-4.48	0.1872	140	0.155	2842	X-RAY DIFFRACTION	100
4.48-4.93	0.1971	147	0.1574	2834	X-RAY DIFFRACTION	100
4.93-5.64	0.2225	157	0.1865	2831	X-RAY DIFFRACTION	100
5.64-7.1	0.2291	132	0.1944	2884	X-RAY DIFFRACTION	99
7.1-45.12	0.2223	161	0.1747	2896	X-RAY DIFFRACTION	96

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	2.511	0.0458	0.9937	2.55	-0.9837	3.0692	0.172	0.0781	0.1467	0.1541	0.084	0.956	-0.3881	-0.6023	-0.2825	0.6737	0.1374	-0.0143	0.7396	-0.0453	1.0786	114.5814	69.7417	131.2674
2	0.9363	-2.0814	1.0859	8.7964	-3.567	1.4659	0.392	0.6373	-0.1126	-1.1663	-0.405	0.7354	0.1545	0.2774	0.0013	1.031	0.1461	-0.2381	0.8224	-0.0094	0.8018	121.7368	55.6716	118.8634
3	2.8601	2.7142	0.269	8.2808	2.3286	4.5326	0.2541	-0.0469	0.1755	0.3412	-0.4603	0.9452	0.0012	-0.0265	0.2412	0.6536	0.1314	-0.0784	0.6066	-0.0322	0.8503	124.8738	54.7504	133.2802
4	9.4285	2.9221	-1.4029	3.8769	0.0547	3.3413	-0.5404	0.557	-0.5122	-0.377	0.7155	-0.2301	0.5816	0.4107	-0.2638	0.8772	0.0526	0.0803	0.4835	-0.0533	0.4912	98.136	83.8958	88.0818
5	4.1536	0.6389	-0.8981	5.1151	1.2273	7.1257	0.0741	-0.0318	0.2802	-0.2544	-0.0493	-0.3084	-0.5976	0.6362	0.001	0.548	-0.0512	0.0445	0.5689	-0.0603	0.5262	105.0916	102.6217	97.7011
6	3.207	0.9864	1.4597	6.0405	-2.2821	6.9615	0.3282	-0.1582	0.5014	-0.1515	-0.2294	-0.04	-0.5406	0.6035	-0.0254	0.5721	-0.0588	0.1573	0.5109	-0.0838	0.5379	104.1007	106.9389	99.699
7	3.9681	3.9441	-2.1934	3.8394	-1.9666	1.8559	0.1682	-0.2623	1.6193	0.0498	0.0992	1.8302	-0.1043	-0.3068	-0.3471	0.7389	0.0535	0.0468	0.625	-0.0757	0.9616	82.9871	101.0655	109.0727
8	2.9883	1.2356	-1.0707	1.1929	-0.4487	0.4396	0.0258	0.2296	0.403	-0.1589	0.281	0.4986	-0.4933	-0.4624	-0.0954	0.7891	-0.0419	0.0274	0.5623	-0.0926	0.7546	86.3731	101.1331	101.4727
9	7.7888	1.0036	2.9379	6.173	0.855	6.1835	0.3262	-0.1289	-0.1639	0.0899	-0.4083	0.1939	0.7243	0.1838	-0.0061	0.5166	0.0654	0.0984	0.443	0.0184	0.5578	91.1452	86.1133	100.3805
10	2.7026	0.3802	-0.1331	0.5886	-1.5799	7.1311	-0.2152	0.5313	-0.0428	-0.078	0.3546	-0.183	-1.1933	-0.4647	-0.1338	0.5673	-0.0074	-0.0161	0.5528	-0.0398	0.5764	87.385	92.737	97.144
11	6.0367	0.2266	0.5424	1.1683	1.1392	1.1428	-0.3609	0.157	1.0048	0.0036	-0.1756	-0.3393	-0.5764	-0.3056	0.5859	1.0543	-0.0789	-0.0097	0.5241	0.0897	0.7986	95.1493	53.5725	89.8683
12	2.7323	-0.3686	0.2462	3.3324	0.6398	6.6389	-0.0427	-0.2477	-0.1186	-0.0058	0.0198	-0.0057	0.4201	0.2886	0.0268	0.5417	-0.0313	0.0136	0.426	0.1333	0.5186	97.2614	37.2378	106.2295
13	1.6695	0.339	-1.0755	2.5545	0.224	4.8347	0.1336	0.137	-0.1752	0.3354	-0.1008	0.316	1.2218	-0.8679	-0.0362	0.8759	-0.1449	0.0427	0.6229	0.0604	0.6297	86.7213	27.8407	90.9346
14	8.3321	-2.4244	0.2696	5.3197	-1.2949	3.1268	-0.092	0.4804	0.1918	-0.2895	-0.0304	-0.3619	0.3373	0.3818	0.185	0.6737	-0.0269	0.0241	0.6025	0.0029	0.5865	95.2972	40.486	84.0788
15	0.0546	0.1778	0.4391	2.9627	0.3962	2.8855	0.1075	-0.2187	-0.5271	-0.0909	-0.2852	0.5389	0.4763	-0.3343	0.1656	0.7596	-0.1377	-0.1037	0.6233	0.0471	0.6136	88.6438	38.2421	87.4349
16	4.1222	1.978	-2.6974	5.2051	-0.1992	8.3541	-0.0463	-0.0423	-0.4865	0.3979	-0.153	-0.1428	0.3505	0.4406	0.2811	0.5837	0.0755	-0.0578	0.4905	0.0724	0.6777	51.9781	77.8326	133.9345
17	5.4666	2.5629	1.1977	5.4587	1.1669	5.9896	-0.3156	0.6544	-0.1896	-0.5145	0.2703	-0.2906	-0.375	0.4643	0.0502	0.6121	-0.0674	-0.0121	0.6143	0.0517	0.4726	51.97	87.8983	118.876
18	0.5565	0.8463	0.4218	1.5059	1.8357	8.1271	-0.0106	-0.0903	0.1609	-0.0102	-0.1149	0.3844	-1.0014	-1.0092	0.1889	0.8712	0.1541	-0.0531	0.6374	0.1055	0.6218	42.4378	96.5377	131.5891
19	6.1575	2.8084	-2.3354	4.5818	-2.6204	4.0344	0.0523	-0.5071	0.6874	0.6623	-0.0341	-0.0308	-0.4208	0.6297	-0.0782	0.6732	0.067	-0.0737	0.5809	-0.0308	0.5838	49.9301	87.9127	144.4097
20	0.2318	-0.2777	0.8671	2.5024	1.0573	4.5077	-0.2009	-0.0829	0.1038	-0.4313	-0.3425	0.4646	-0.1712	-0.3447	0.4862	0.717	0.0379	0.0344	0.4996	0.0007	0.5885	43.4541	89.5997	140.675
21	7.0467	1.7251	0.6476	2.973	-0.6102	4.0753	-0.3815	0.6159	0.6265	-0.0358	0.5209	0.3581	-1.1408	-0.0123	-0.2402	0.997	0.19	-0.0012	0.596	0.0269	0.5712	43.9153	110.6376	85.0707
22	4.4084	1.6598	-0.6568	6.2405	-2.6627	7.1145	0.2051	-0.0743	-0.5229	-0.0909	0.1348	0.3681	0.6441	-0.6921	-0.3258	0.4824	-0.0074	-0.1337	0.5343	-0.0014	0.593	36.7481	89.2597	91.7724
23	2.6497	2.2348	1.5965	5.6576	2.949	5.3157	0.3149	0.1065	-0.9283	0.3189	0.2352	-1.1281	0.6788	0.6199	-0.6652	0.5849	0.1426	-0.079	0.5711	-0.005	0.7279	53.915	87.4411	93.0762
24	3.6973	1.8738	-1.2444	4.3885	-1.6027	0.8204	0.6216	0.1419	-0.4388	0.4072	-0.2541	-0.761	0.6469	0.9733	-0.121	0.5146	0.1303	-0.0763	0.427	0.0908	0.6158	57.6022	96.7643	97.7993
25	6.0519	3.994	-1.6568	7.3614	-4.5173	9.9639	0.3781	-0.1332	0.4282	0.2963	0.1479	0.1922	-0.7724	-0.2889	-0.5602	0.5516	0.1907	-0.0152	0.48	-0.0445	0.4915	51.2529	106.028	96.5663
26	4.7489	1.7787	3.002	1.7062	-0.8553	6.7715	0.1108	0.3735	-0.2525	-0.0368	-0.1075	-0.3983	-0.0311	0.432	-0.0857	0.5072	0.0837	0.0095	0.5575	0.0046	0.691	55.1796	99.4627	91.582
27	4.9799	-1.9827	-1.8649	5.8932	1.1545	6.1363	-0.0346	0.9843	-0.0008	-0.489	-0.1566	-0.0082	0.1769	-1.0069	0.1933	0.9513	-0.0143	-0.1814	0.6945	-0.0495	0.5772	80.5574	63.3686	90.8446
28	3.6356	0.2311	0.2227	3.7014	0.0951	3.8646	0.0442	0.0821	-0.314	0.1465	0.0003	0.9542	0.3562	-0.8806	-0.0532	0.6671	-0.1473	-0.0803	0.7718	0.0083	0.9844	63.7953	55.0957	104.8998
29	7.7745	5.9665	-0.5796	6.2767	0.4926	0.7619	1.7872	-1.1227	-0.849	2.56	-1.6215	-0.484	0.0235	0.4142	-0.1979	1.2863	-0.1189	0.0082	0.6527	-0.0368	0.7929	74.8346	70.663	120.0621
30	0.4468	1.2244	0.0609	7.046	-0.6205	0.1719	-0.157	-0.325	0.0172	1.0494	-0.3203	-0.9528	0.0655	0.121	0.0272	0.9927	-0.0989	-0.0672	0.7466	0.0044	0.9695	74.9616	59.0889	117.5877
31	0.7095	1.231	0.1393	5.1919	-0.5742	0.9905	0.1882	-0.2182	0.3447	0.7058	-0.0156	0.2841	0.3529	0.2581	0.0272	0.7768	-0.0258	-0.0419	0.6868	0.0324	0.7191	77.9311	70.4266	112.5555
32	3.2322	-0.8428	-3.0255	8.1711	1.514	6.3524	0.2803	0.3378	0.2	-0.7161	-0.3012	0.6634	-0.4552	-0.3205	0.0047	0.7173	-0.0542	-0.1685	0.4622	-0.042	0.6513	77.7757	72.4613	101.4434
33	1.4923	-0.4986	0.35	1.3967	0.2606	2.3479	0.2498	-0.3063	-0.46	-0.4213	-0.1146	0.3749	0.6699	-0.2605	-0.0921	0.6729	-0.1603	-0.0461	0.6376	0.0057	0.7667	79.7252	68.4193	106.8419

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 141 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 142 through 203 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 204 through 264 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 28 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 29 through 108 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 109 through 141 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 142 through 162 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 163 through 203 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 204 through 242 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 243 through 266 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 28 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 29 through 141 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 142 through 203 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 204 through 242 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 243 through 265 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 2 through 66 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 67 through 127 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 128 through 194 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 204 through 242 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 243 through 265 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 2 through 28 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 29 through 127 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 128 through 179 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 180 through 203 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 204 through 242 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 243 through 267 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 2 through 28 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 29 through 141 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 142 through 162 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 163 through 179 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 180 through 203 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 204 through 242 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 243 through 264 )

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