PDB-7e4s: Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-he...

ID or keywords:

Entry

Database: PDB / ID: 7e4s

Title

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

Components

5-dehydro-4-deoxy-D-glucuronate isomerase

Keywords

ISOMERASE / 4-deoxy-L-threo-5-hexosulose-uronate / cupin

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: 2.79 Å

Authors

Yamamoto, Y. / Takase, R. / Mikami, B. / 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	Feb 15, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 23, 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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Download

PDBx/mmCIF format	7e4s.cif.gz	681.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7e4s.ent.gz	570.2 KB	Display	PDB format
PDBx/mmJSON format	7e4s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7e4s_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	7e4s_full_validation.pdf.gz	1.4 MB	Display
Data in XML	7e4s_validation.xml.gz	60.2 KB	Display
Data in CIF	7e4s_validation.cif.gz	78.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e4/7e4s ftp://data.pdbj.org/pub/pdb/validation_reports/e4/7e4s	HTTPS FTP

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Related structure data

Related structure data	7vgkC 1ywkS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1xru-1 2zs1-2 347 1x9f-d 6znt-d 6hsh-d Search similar-shape structures by Omokage search (details) 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: 5-dehydro-4-deoxy-D-glucuronate isomerase

B: 5-dehydro-4-deoxy-D-glucuronate isomerase

C: 5-dehydro-4-deoxy-D-glucuronate isomerase

D: 5-dehydro-4-deoxy-D-glucuronate isomerase

E: 5-dehydro-4-deoxy-D-glucuronate isomerase

F: 5-dehydro-4-deoxy-D-glucuronate isomerase

hetero molecules

202 kDa, 6 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)	94.290, 189.250, 117.800
Angle α, β, γ (deg.)	90.00, 106.24, 90.00
Int Tables number	5
Space group name H-M	C121
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	5-dehydro-4-deoxy-D-glucuronate isomerase Mass: 33331.629 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: Lc 705 / Gene: kduI1, kduI, GKD15_03440, LRHP344_00167 / Production host: Escherichia coli (E. coli) References: UniProt: A0A508YKK7, 5-dehydro-4-deoxy-D-glucuronate isomerase
#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.52 Å³/Da / Density % sol: 51.25 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES, 1 mM 4-deoxy-L-threo-5-hexosulose-uronate, 1 mM rhamnose,10% PEG 6000, 25% ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 25, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.79→47.31 Å / Num. obs: 48121 / % possible obs: 98.1 % / Redundancy: 3.16 % / CC_1/2: 0.989 / Net I/σ(I): 9.5
Reflection shell	Resolution: 2.79→2.96 Å / Num. unique obs: 7729 / CC_1/2: 0.414

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
XDS		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YWK

1ywk

Resolution: 2.79→47.31 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2382	2401	5 %
R_work	0.1646	-	-
obs	0.1682	48012	97.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.79→47.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13229	0	96	31	13356

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	13669
X-RAY DIFFRACTION	f_angle_d	1.103	18513
X-RAY DIFFRACTION	f_dihedral_angle_d	20.313	5037
X-RAY DIFFRACTION	f_chiral_restr	0.062	1948
X-RAY DIFFRACTION	f_plane_restr	0.007	2392

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 (%)
2.79-2.85	0.4463	136	0.386	2602	X-RAY DIFFRACTION	95
2.85-2.91	0.3669	141	0.356	2659	X-RAY DIFFRACTION	99
2.91-2.98	0.409	142	0.3377	2698	X-RAY DIFFRACTION	99
2.98-3.05	0.3587	144	0.3307	2740	X-RAY DIFFRACTION	99
3.05-3.14	0.4002	143	0.3228	2717	X-RAY DIFFRACTION	99
3.14-3.23	0.4837	142	0.3834	2683	X-RAY DIFFRACTION	99
3.23-3.33	0.363	141	0.3066	2690	X-RAY DIFFRACTION	98
3.33-3.45	0.269	142	0.2044	2698	X-RAY DIFFRACTION	99
3.45-3.59	0.2499	143	0.1684	2707	X-RAY DIFFRACTION	99
3.59-3.75	0.2426	142	0.1522	2710	X-RAY DIFFRACTION	99
3.75-3.95	0.24	143	0.1495	2716	X-RAY DIFFRACTION	99
3.95-4.2	0.1894	141	0.1351	2675	X-RAY DIFFRACTION	98
4.2-4.52	0.2015	141	0.113	2670	X-RAY DIFFRACTION	97
4.52-4.98	0.2018	140	0.1092	2664	X-RAY DIFFRACTION	97
4.98-5.7	0.1899	141	0.1191	2684	X-RAY DIFFRACTION	98
5.7-7.17	0.2202	142	0.1358	2690	X-RAY DIFFRACTION	98
7.17-47.31	0.1637	137	0.1175	2608	X-RAY DIFFRACTION	93

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	4.0428	0.0374	1.2852	3.8697	1.8399	2.7291	-0.1679	0.2834	-0.4099	-0.4533	0.1748	0.5296	0.0501	-0.1628	-0.009	0.5524	-0.1016	0.0871	0.5238	0.0397	0.7093	17.2855	-95.7245	23.2808
2	1.164	-2.4552	0.0538	7.8472	-0.4401	-0.0117	-0.6678	-0.6969	-0.7497	1.0208	0.4832	2.0316	0.1465	-0.0707	0.2568	0.8381	0.0958	0.3107	0.7698	0.1461	1.2684	6.7399	-95.1689	40.94
3	3.112	-4.6578	0.043	8.628	-1.4617	0.9947	-0.6513	-0.4009	-0.1049	0.9437	0.3121	0.6895	-0.0699	-0.0744	0.1625	0.5689	0.0391	0.1197	0.5967	0.0343	0.8074	11.4708	-86.0371	38.3644
4	7.7736	-0.3742	2.3061	4.5022	0.2104	3.5826	-0.147	-0.3071	-0.2641	0.3826	0.1844	0.3682	0.1965	-0.3209	-0.0486	0.4988	0.0315	0.1348	0.4636	0.0778	0.695	14.053	-81.188	36.3712
5	2.1152	0.4515	0.1	0.4073	-1.091	3.3669	-0.1856	-0.3299	0.0887	0.1154	0.1362	-0.2291	-0.4439	-0.005	0.0085	0.6658	0.1221	0.1208	0.5072	-0.0284	0.7132	41.7926	-83.5658	38.6649
6	8.5245	1.7268	0.5066	4.7862	-0.1559	3.959	-0.0943	-1.0459	-0.7516	0.2569	-0.1315	-0.5372	0.2433	0.3309	0.3195	0.6641	0.1051	0.0962	0.6342	0.1812	0.692	45.3493	-100.9977	50.2711
7	2.9995	0.3545	-1.4202	2.3956	-0.3462	1.3696	-0.5306	0.1211	-0.7883	-0.4696	0.0442	-0.5917	0.6839	0.4312	0.4398	0.6784	0.0264	0.2075	0.551	0.0479	0.9202	48.8997	-104.2019	32.673
8	4.709	0.6216	-0.994	2.9929	-0.7639	2.2651	-0.3636	0.4651	0.2471	-0.5359	0.0954	-0.4091	0.3958	0.3278	0.1777	0.6859	-0.0465	0.2193	0.5136	0.032	0.8637	50.6311	-94.3209	27.3292
9	5.4122	1.1503	-0.2474	2.7433	-1.6604	3.1401	0.1133	0.3077	-0.2407	-0.4953	-0.1726	-0.677	0.3428	0.3122	0.034	0.611	0.0947	0.1806	0.4669	-0.0274	0.7175	49.5407	-88.6398	26.7916
10	2.5159	-0.1024	1.1429	7.0893	-0.7413	0.7656	0.1306	0.5889	-0.1221	-0.6045	-0.2535	-0.3294	0.1512	-0.162	0.1079	0.7206	-0.0631	0.289	0.579	-0.0196	0.7983	51.3326	-66.0443	10.9419
11	3.9615	-0.9516	0.7823	1.8932	0.1014	2.0306	-0.1928	1.016	0.0443	-1.4525	0.1211	-0.9971	0.1686	0.2792	0.001	1.2357	-0.0132	0.5994	0.8437	0.0352	1.0335	67.8276	-62.5418	-1.9853
12	1.4783	0.1018	-1.1239	8.9022	-7.968	7.7848	0.6576	-0.3013	-0.1195	-0.0187	-1.2952	-1.2992	-0.6264	1.7227	0.7093	0.8802	-0.0289	0.3278	0.7705	0.0949	1.3869	76.8896	-79.171	14.4092
13	3.5116	0.8293	-2.086	1.8206	-1.6754	2.7599	0.062	-0.1073	0.4368	-0.1153	-0.2883	-0.6105	0.133	0.516	0.2111	0.794	-0.0739	0.4017	0.6153	-0.0101	1.2956	71.0055	-71.1999	15.2712
14	5.0928	-0.3412	-2.4138	2.6215	-0.7354	5.0845	-0.3448	0.4001	-0.2036	0.1065	-0.068	-0.2334	1.0895	-0.1396	0.1125	0.7616	-0.0785	0.2571	0.4897	-0.011	0.9365	56.2952	-77.895	17.7849
15	0.1746	0.6051	-0.1829	4.5931	-0.377	1.6958	-0.234	0.2681	-0.3727	-0.8573	0.3796	-0.0711	0.0349	0.5936	0.0951	0.7273	-0.0039	0.3053	0.6611	0.0381	0.9513	59.3945	-71.865	16.2471
16	0.1377	0.9378	-0.0658	6.3243	-0.2621	2.7305	-0.1756	0.3983	0.1257	-0.0615	-0.1313	-1.0497	0.0255	0.1896	0.25	0.6429	0.0517	0.2954	0.7273	0.132	1.3969	68.0071	-69.9993	21.3725
17	4.6299	-0.5705	0.5354	3.3825	1.3188	2.7237	0.0285	-0.4136	-0.1152	0.1143	-0.1525	-0.8534	0.0124	0.246	0.1181	0.5085	-0.0328	0.02	0.4914	0.0685	0.7728	65.458	-41.1313	27.7867
18	5.1289	-2.8982	-1.5625	3.1354	-0.2179	1.7347	-0.1038	0.4345	0.1302	-0.3697	-0.0899	-0.6119	0.0683	0.137	0.265	0.5352	-0.0899	0.1213	0.6057	-0.0449	0.8377	59.0083	-31.876	15.658
19	4.974	-3.411	0.7415	7.3043	2.485	4.4207	-0.2583	0.5016	0.0434	-0.4119	-0.098	-0.4003	0.0889	0.2617	0.2969	0.4423	-0.0868	0.141	0.5315	0.0168	0.5294	49.1654	-39.194	18.8542
20	3.2398	2.7633	3.3286	4.0202	-0.2229	9.0434	-0.377	-0.3064	-0.6221	-0.0789	0.0773	0.3023	0.2843	1.3419	0.4757	0.5772	0.1505	0.1081	0.6816	0.0517	0.6918	21.2594	-54.681	36.4817
21	5.3345	-0.5775	-2.1271	4.7245	-0.8532	5.18	0.1632	-0.6462	0.1625	1.3136	0.0577	0.2272	-0.6857	0.103	-0.1871	0.7914	0.0865	0.0532	0.6064	0.0019	0.4697	11.0604	-42.7904	47.37
22	6.7462	2.7194	-3.371	5.6051	-1.2301	6.5354	0.0518	-1.0732	0.1587	1.8163	0.0343	0.9491	-0.3302	-0.3685	0.0128	1.208	0.3003	0.3378	1.03	0.0027	0.719	-0.1159	-42.581	55.13
23	7.3672	-0.1645	-4.4868	1.0489	1.4998	4.6411	0.231	-0.514	0.7522	1.5875	0.5694	1.5148	-1.1477	-0.9367	-0.8001	0.8072	0.1103	0.3752	0.6662	0.0917	0.9262	1.7875	-39.357	41.1122
24	1.3147	2.076	-0.2608	4.8509	-0.9965	0.22	0.0957	-0.0154	-0.3044	0.2671	0.0877	1.0722	-0.1773	-0.4654	-0.1418	0.7296	0.1803	0.1283	0.8029	0.2007	1.1529	-7.6308	-54.9013	40.1052
25	6.3465	-4.0226	2.3884	2.7336	-1.8449	1.4065	0.5866	0.1269	-0.2436	-0.5349	-0.4317	1.3367	0.262	0.7187	-0.1066	0.9103	0.1633	0.3619	0.7475	0.0521	0.8452	-0.2467	-60.7484	37.131
26	6.2951	0.9587	-2.6507	7.5133	0.1305	7.1036	-0.0974	-0.347	-0.2176	0.4368	0.175	0.2026	0.4193	-0.3638	-0.0615	0.483	0.1192	0.0991	0.5034	0.0937	0.6035	9.0516	-62.4625	39.2263
27	9.1532	-0.4487	-3.6007	9.7522	0.6877	1.6303	-0.2511	1.4866	-0.1638	-0.3671	0.3419	1.9265	0.322	-0.2956	-0.017	0.5161	0.0359	-0.1971	0.9977	-0.1256	0.9652	2.8235	-56.085	30.8525
28	4.4152	1.6134	-2.3157	3.0561	-1.2163	2.1129	-0.148	1.5815	0.7122	-0.3184	0.6476	0.5841	-0.0051	-0.8006	-0.3566	0.57	0.0035	-0.0499	1.0936	0.218	0.6134	13.0137	-32.9698	15.8335
29	6.7333	2.4941	-1.7339	6.3587	-3.9592	2.5367	-0.2163	0.3756	0.1995	0.1612	0.3775	-0.1527	-0.0854	-0.3006	-0.1028	0.5185	0.1241	0.0635	0.6295	-0.0116	0.4739	28.7802	-33.3146	20.3578
30	8.7231	2.9964	-1.7964	1.2125	-1.3886	2.8666	0.2248	-0.8002	0.4016	0.6839	0.0701	-0.0915	-0.2579	0.1404	-0.2979	0.7979	0.1491	0.0155	0.6312	-0.036	0.7375	25.752	-29.8575	27.8053

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 179 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 180 through 210 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 211 through 280 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 54 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 55 through 127 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 128 through 179 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 180 through 210 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 211 through 280 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 2 through 38 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 39 through 141 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 142 through 162 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 163 through 210 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 211 through 234 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 235 through 252 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 253 through 280 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 127 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 128 through 218 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 219 through 266 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 2 through 28 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 29 through 84 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 85 through 127 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 128 through 141 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 142 through 179 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 180 through 202 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 203 through 256 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 257 through 280 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 2 through 179 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 180 through 252 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 253 through 280 )

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