PDB-6dkh: The crystal structure of L-idonate 5-dehydrogenase from Escherich...

ID or keywords:

Entry

Database: PDB / ID: 6dkh

Title

The crystal structure of L-idonate 5-dehydrogenase from Escherichia coli str. K-12 substr. MG1655

Components

L-idonate 5-dehydrogenase (NAD(P)(+))

Keywords

OXIDOREDUCTASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

L-idonate 5-dehydrogenase / L-idonate catabolic process / L-idonate 5-dehydrogenase [NAD(P)+] activity / L-idonate 5-dehydrogenase (NAD+) activity / D-gluconate metabolic process / metal ion binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.608 Å

Authors

Tan, K. / Evdokimova, E. / McChesney, C. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The crystal structure of L-idonate 5-dehydrogenase from Escherichia coli str. K-12 substr. MG1655
Authors: Tan, K. / Evdokimova, E. / McChesney, C. / Savchenko, A. / Joachimiak, A.

History

Deposition	May 29, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 6, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6dkh.cif.gz	532.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6dkh.ent.gz	441.8 KB	Display	PDB format
PDBx/mmJSON format	6dkh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6dkh_validation.pdf.gz	450 KB	Display	wwPDB validaton report
Full document	6dkh_full_validation.pdf.gz	457.6 KB	Display
Data in XML	6dkh_validation.xml.gz	45.5 KB	Display
Data in CIF	6dkh_validation.cif.gz	61.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dk/6dkh ftp://data.pdbj.org/pub/pdb/validation_reports/dk/6dkh	HTTPS FTP

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Related structure data

Related structure data	1e3jS S: Starting model for refinement
Similar structure data	1teh-1 4z5r-8 4z5r-2 7av7-3 4dl9-d 4rqu-d 7aas-2 4dla-d 4m1g-d 5utz-1 2fzw-d 7aau-1 7av7-2 6ohg-d 1qlh-1 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
Other databases	TargetTrack: CSGID-IDP96074

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#13 - Jan 2001 Alcohol Dehydrogenase similarity (5) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: L-idonate 5-dehydrogenase (NAD(P)(+))

B: L-idonate 5-dehydrogenase (NAD(P)(+))

C: L-idonate 5-dehydrogenase (NAD(P)(+))

D: L-idonate 5-dehydrogenase (NAD(P)(+))

hetero molecules

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

1

A: L-idonate 5-dehydrogenase (NAD(P)(+))

D: L-idonate 5-dehydrogenase (NAD(P)(+))

hetero molecules

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

2

B: L-idonate 5-dehydrogenase (NAD(P)(+))

C: L-idonate 5-dehydrogenase (NAD(P)(+))

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.055, 77.646, 128.350
Angle α, β, γ (deg.)	90.00, 92.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	L-idonate 5-dehydrogenase (NAD(P)(+)) Mass: 37458.809 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: idnD, yjgV, b4267, JW4224 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: P39346, L-idonate 5-dehydrogenase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.57 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris, 28% PEG4000, 2.5 mM NADPH

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97894 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2017
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97894 Å / Relative weight: 1
Reflection	Resolution: 2.608→49.5 Å / Num. obs: 45516 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / B_iso Wilson estimate: 51.7 Å² / R_merge(I) obs: 0.097 / R_pim(I) all: 0.061 / R_rim(I) all: 0.115 / Χ²: 1.168 / Net I/σ(I): 14.5
Reflection shell	Resolution: 2.608→2.64 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.764 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2268 / CC_1/2: 0.682 / R_pim(I) all: 0.475 / R_rim(I) all: 0.901 / Χ²: 0.537 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1E3J

1e3j

Resolution: 2.608→38.987 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.73

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2592	2284	5.02 %	random
R_work	0.1997	-	-	-
obs	0.2028	45461	96.73 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.608→38.987 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10401	0	4	20	10425

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	10621
X-RAY DIFFRACTION	f_angle_d	0.45	14386
X-RAY DIFFRACTION	f_dihedral_angle_d	16.066	6320
X-RAY DIFFRACTION	f_chiral_restr	0.044	1614
X-RAY DIFFRACTION	f_plane_restr	0.003	1875

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 (%)
2.6083-2.665	0.3258	122	0.2916	2657	X-RAY DIFFRACTION	96
2.665-2.727	0.3875	173	0.2768	2710	X-RAY DIFFRACTION	98
2.727-2.7952	0.3253	189	0.2702	2663	X-RAY DIFFRACTION	98
2.7952-2.8707	0.3827	126	0.2731	2725	X-RAY DIFFRACTION	98
2.8707-2.9552	0.3329	132	0.2729	2710	X-RAY DIFFRACTION	97
2.9552-3.0505	0.3485	116	0.2525	2718	X-RAY DIFFRACTION	97
3.0505-3.1595	0.3424	111	0.2526	2564	X-RAY DIFFRACTION	92
3.1595-3.2859	0.3127	123	0.2466	2773	X-RAY DIFFRACTION	99
3.2859-3.4354	0.2989	116	0.2414	2776	X-RAY DIFFRACTION	99
3.4354-3.6164	0.3161	133	0.2204	2717	X-RAY DIFFRACTION	98
3.6164-3.8428	0.2362	147	0.19	2723	X-RAY DIFFRACTION	98
3.8428-4.1392	0.2505	161	0.1838	2599	X-RAY DIFFRACTION	94
4.1392-4.5551	0.2162	135	0.156	2774	X-RAY DIFFRACTION	99
4.5551-5.213	0.2199	186	0.1523	2722	X-RAY DIFFRACTION	98
5.213-6.5627	0.2293	162	0.1774	2647	X-RAY DIFFRACTION	95
6.5627-38.9912	0.2047	152	0.1649	2699	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	2.3363	0.4659	0.535	3.8437	-0.0097	2.612	0.0829	-0.8512	-0.0161	1.3419	-0.2692	0.3037	0.0325	-0.3239	0.1895	0.8206	0.0198	0.1018	0.9626	0.2536	0.492	33.7568	-0.7608	61.8864
2	2.0302	0.2653	0.5133	2.0152	1.7778	2.3276	0.0164	-0.112	-0.4007	0.4252	0.2428	0.0469	0.4147	-0.3656	-0.2467	0.5466	-0.0221	0.0259	0.7526	0.2561	0.6051	40.4086	-5.3114	50.5021
3	3.3101	-0.4359	0.6286	1.5614	0.9995	1.1311	-0.0353	-0.7359	-0.2908	0.4187	0.0873	0.126	-0.0141	-0.4557	-0.0633	0.5421	0.0287	0.0391	0.7472	0.1628	0.3957	44.0619	7.684	53.5026
4	3.9054	-0.8675	-0.9458	2.3112	-0.1303	1.9925	-0.1527	-0.1852	-0.2948	-0.1442	0.1589	-0.2042	0.0878	-0.1226	-0.0097	0.3174	-0.0037	0.0245	0.3311	0.0666	0.3281	44.8464	5.5651	32.2442
5	4.5407	1.0788	-0.417	7.8235	1.152	1.9989	0.3374	-0.3351	-0.2192	-0.1826	-0.5395	0.4263	0.1311	-0.5765	0.2032	0.3015	-0.1029	-0.056	0.6362	0.0539	0.539	40.7384	-2.1304	23.4913
6	2.4785	1.7684	-0.6345	2.0547	1.4576	3.8282	-0.0262	0.6479	-0.8484	-0.3153	0.0894	-0.0148	0.4374	-0.0098	-0.0124	0.5034	-0.0025	-0.0044	0.4991	-0.0187	0.6038	50.5755	-4.0216	19.9768
7	7.2087	0.6478	-1.0109	4.4841	1.3119	4.3683	0.022	-0.7257	-1.318	-0.1338	0.0377	-0.2354	0.8023	0.1666	-0.0823	0.4739	-0.0231	0.0232	0.4451	0.1266	0.743	60.2312	-5.9498	27.9858
8	1.8862	-0.7234	0.0027	1.0677	0.2399	2.1507	0.1016	-0.2975	-0.1861	0.034	0.0694	0.091	0.1541	-0.2421	-0.169	0.3626	0.0027	-0.0046	0.3697	0.0835	0.3105	42.2367	5.6034	37.7473
9	4.0836	0.0249	-0.8121	3.2604	-1.4489	8.8605	0.2871	-0.4063	-1.1485	-0.058	0.3502	0.4209	1.3022	-1.5006	-0.3407	0.5698	-0.1413	-0.0421	0.6979	0.3007	0.5948	31.1175	-9.5688	43.2964
10	2.2741	0.6934	-0.0807	3.7539	0.3734	0.5957	-0.0113	0.8292	0.025	-0.9511	-0.0533	-0.3186	-0.016	-0.2333	0.1328	0.7904	-0.0423	0.001	0.7437	0.1095	0.3485	36.9482	31.8358	-1.7932
11	2.9704	-0.9705	0.4919	2.0917	-0.2062	1.741	-0.0305	0.3604	0.0151	-0.0625	0.1546	-0.1675	-0.0427	-0.0758	-0.1187	0.3358	-0.0624	0.0259	0.4682	0.0167	0.2653	42.5297	29.9963	8.792
12	8.1699	-5.1348	0.7971	4.3627	0.5564	1.3136	0.4819	0.0565	0.0366	-0.7558	0.0815	-0.413	0.3219	-0.1116	-0.5734	0.4007	-0.0375	0.0042	0.4603	0.1021	0.4582	56.6345	25.0672	10.8518
13	3.0201	0.6396	-0.8392	5.3466	-2.1287	3.4335	0.086	0.5595	-0.0597	-0.0435	-0.2591	-0.1397	-0.0541	-0.3074	0.2283	0.5121	-0.0419	-0.012	0.468	-0.0773	0.3184	40.705	26.0897	6.683
14	4.0503	0.3207	2.4224	0.4392	1.1461	4.1419	-0.1604	-0.4363	0.3246	0.0058	0.0463	-0.065	-0.0794	-0.3859	0.1335	0.3532	0.055	0.0334	0.3282	0.029	0.4063	43.4576	27.808	31.4179
15	8.3711	0.3624	1.9172	2.2338	0.4614	2.1956	-0.1622	-1.1498	0.8943	0.5833	-0.1743	-0.1479	-0.2858	-0.5264	0.2691	0.572	0.12	-0.0183	0.4666	-0.0912	0.497	49.2449	35.1824	41.6469
16	5.9327	0.7324	2.3249	3.1024	0.8752	4.1373	-0.1436	0.2343	1.0203	0.0785	0.1754	-0.1872	-0.6484	0.3237	0.1401	0.4629	-0.014	0.0063	0.4121	-0.0215	0.6686	60.1361	36.156	34.478
17	2.659	-0.0753	0.2323	2.7879	-0.9051	4.5065	0.0799	0.2351	0.1575	0.0035	-0.0115	0.1944	-0.3945	-0.3988	-0.0463	0.3713	0.0364	0.0156	0.3353	0.04	0.3433	35.9749	31.3857	19.253
18	2.3982	0.8694	0.5093	4.1784	0.4395	2.8667	-0.1828	-1.0462	0.4694	0.5372	0.0119	0.3682	-0.491	0.3124	0.1595	0.7548	0.1174	-0.0605	1.0773	-0.2862	0.6111	90.9408	37.0936	61.3569
19	2.7851	-0.107	-0.0968	5.9452	0.0841	3.0668	-0.0676	-0.4828	0.9046	-0.4359	-0.0108	1.7961	-0.8071	-0.4663	0.1301	0.8961	0.0512	-0.2946	0.7188	-0.1883	1.2523	83.1506	44.1716	45.7173
20	3.5491	1.6458	0.6324	0.7625	0.5484	2.6132	0.1438	-1.1151	0.4511	0.1296	0.0386	0.124	0.3108	0.0942	-0.0124	0.5107	0.0752	-0.0468	0.805	-0.1035	0.5699	86.0742	26.7923	55.5474
21	8.7542	1.2603	1.4257	0.5865	-0.5678	2.2639	-0.2015	-0.6417	1.1696	0.2427	0.1535	-0.0889	0.1172	0.1067	0.1135	0.494	0.1317	-0.0858	0.6784	-0.1396	0.6911	70.7045	29.1613	50.2264
22	3.6014	0.2934	0.7071	3.3943	1.3354	4.7511	-0.037	-0.9483	0.5249	0.4784	-0.0782	0.4152	-0.1641	0.7131	0.0696	0.449	-0.0424	0.0038	0.8207	-0.0908	0.6584	86.6132	30.4953	54.2433
23	2.6384	-0.905	1.6408	0.7705	0.1862	4.2411	-0.124	0.3315	0.5577	-0.0299	0.0082	-0.0233	-0.4113	0.5632	0.103	0.3874	-0.0543	-0.0323	0.3653	0.0318	0.5222	84.1504	27.7001	28.6072
24	7.249	0.6085	1.2442	2.5334	-0.22	4.1053	-0.2734	0.9658	1.1189	-0.553	0.2208	0.2081	-0.6792	0.4106	0.0516	0.5991	-0.0381	-0.0436	0.4699	0.1631	0.5901	76.0561	33.9221	17.4171
25	7.8218	0.8131	1.5831	2.8988	0.0118	4.3257	-0.0893	-0.2905	1.144	0.0021	-0.0646	0.1741	-0.4274	0.0479	0.0936	0.4807	-0.018	-0.0284	0.3398	0.0318	0.5413	67.2936	35.1502	24.888
26	3.6082	0.5815	0.4452	2.7082	1.8641	3.6236	-0.2769	0.065	0.8331	-0.2288	0.2759	-0.3213	-0.6731	0.3418	-0.0107	0.467	-0.0851	-0.0864	0.4594	0.046	0.5581	91.2797	33.2555	40.7855
27	2.4836	-0.2443	0.7552	1.9624	-0.461	2.3056	-0.1797	0.5808	-0.2564	-0.4146	0.1179	0.1568	0.1755	0.2415	0.0241	0.491	-0.0702	0.0898	0.7217	-0.0843	0.543	89.3698	-3.4738	10.0964
28	4.1626	-1.5122	1.3738	2.7941	-1.338	2.2249	0.1699	0.0246	-0.3292	-0.6589	0.0463	0.374	-0.2415	-0.1029	-0.053	0.4709	0.0015	0.0054	0.5081	0.0498	0.5702	72.6615	2.4518	13.5862
29	4.6858	-0.3552	-0.7071	2.4976	-0.1764	4.2736	-0.0285	0.9009	-0.5141	-0.717	-0.307	0.3404	0.264	0.0379	0.0548	0.5689	0.0385	0.0534	0.554	-0.0477	0.4831	88.7502	1.0819	11.1194
30	4.6521	-0.4919	-1.9908	1.2479	0.3855	3.4859	-0.1064	0.1326	-0.0205	-0.0378	0.0845	0.0287	0.028	-0.2987	-0.0031	0.3182	0.0218	0.0368	0.263	0.0479	0.3749	81.8431	5.5208	31.8553
31	4.1237	-0.7269	-0.6642	1.8986	-0.7218	4.4951	0.0304	-0.6645	-0.3195	0.0919	-0.0466	-0.5138	0.1922	0.7264	0.0419	0.3373	-0.0021	0.053	0.6402	0.1033	0.4903	85.5939	2.1221	40.4989
32	7.4034	-0.9794	-0.9288	4.0091	-0.7684	4.1919	0.0145	-0.3659	-1.1156	-0.029	-0.0989	0.2095	0.5146	0.0652	0.0809	0.4355	-0.0245	0.0686	0.4405	0.1441	0.5571	70.6111	-3.7192	42.5866
33	2.2334	0.6165	-1.4618	1.1469	0.1821	3.1779	-0.1845	-0.071	-0.1214	0.0545	0.1356	-0.1724	0.1342	0.2227	-0.0454	0.3165	0.0148	0.0167	0.401	0.0366	0.4004	84.9787	4.6116	27.2573
34	4.2758	0.289	-0.913	4.2845	1.2508	5.388	0.0536	0.0055	-1.2637	0.7903	-0.0698	-0.4383	1.5413	0.886	0.2116	0.7255	0.1767	0.0133	0.605	0.0269	0.9886	96.3621	-11.1785	24.0134

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 34 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 35 through 74 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 75 through 145 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 146 through 192 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 193 through 212 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 213 through 245 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 246 through 282 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 283 through 319 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 320 through 343 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid -1 through 34 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 35 through 96 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 97 through 116 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 117 through 145 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 146 through 212 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 213 through 245 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 246 through 288 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 289 through 343 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid -2 through 34 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 35 through 58 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 59 through 96 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 97 through 116 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 117 through 145 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 146 through 219 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 220 through 245 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 246 through 288 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 289 through 343 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid -2 through 96 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 97 through 116 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 117 through 145 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 146 through 179 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 180 through 219 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 220 through 282 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 283 through 319 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 320 through 343 )

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