PDB-8skb: Crystal Structure of GDP-mannose 3,5 epimerase de Myrciaria dubia...

ID or keywords:

Entry

Database: PDB / ID: 8skb

Title

Crystal Structure of GDP-mannose 3,5 epimerase de Myrciaria dubia in complex with NAD

Components

GDP-mannose 3,5 epimerase

Keywords

PLANT PROTEIN /

GDP-mannose 3 / 5 epimerase /

Enzyme

Function / homology

NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Function and homology information

Biological species

Myrciaria dubia (camu-camu)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.58 Å

Authors

Santillan, J.A.V. / Cabrejos, D.A.L. / Pereira, H.M. / Gomez, J.C.C. / Garratt, R.C.

Funding support

Peru,

Brazil, 3items

Citation

Journal: J.Exp.Bot. / Year: 2024
Title: Structural insights into the Smirnoff-Wheeler pathway for vitamin C production in the Amazon fruit Camu-Camu.
Authors: Vargas, J.A. / Sculaccio, S.A. / Pinto, A.P.A. / Pereira, H.D. / Mendes, L.F.S. / Flores, J.F. / Cobos, M. / Castro, J.C. / Garratt, R.C. / Leonardo, D.A.

History

Deposition	Apr 19, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8skb.cif.gz	527.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8skb.ent.gz	434.1 KB	Display	PDB format
PDBx/mmJSON format	8skb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sk/8skb ftp://data.pdbj.org/pub/pdb/validation_reports/sk/8skb	HTTPS FTP

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Related structure data

Related structure data	7smlC 8sccC 8sg0C 8usuC 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: GDP-mannose 3,5 epimerase

B: GDP-mannose 3,5 epimerase

C: GDP-mannose 3,5 epimerase

D: GDP-mannose 3,5 epimerase

hetero molecules

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

1

A: GDP-mannose 3,5 epimerase

hetero molecules

B: GDP-mannose 3,5 epimerase

hetero molecules

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

2

C: GDP-mannose 3,5 epimerase

hetero molecules

D: GDP-mannose 3,5 epimerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	87.847, 80.042, 107.656
Angle α, β, γ (deg.)	90.00, 95.25, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	GDP-mannose 3,5 epimerase Mass: 46500.715 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myrciaria dubia (camu-camu) / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: GDP-mannose 3,5-epimerase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.03 Å³/Da / Density % sol: 39.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Lithium sulfate, 0.1M Tris pH8.5, 30% w/v PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 9, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97718 Å / Relative weight: 1
Reflection	Resolution: 2.58→107.2 Å / Num. obs: 47036 / % possible obs: 100 % / Redundancy: 6.3 % / CC_1/2: 0.982 / R_merge(I) obs: 0.276 / R_pim(I) all: 0.121 / R_rim(I) all: 0.302 / Χ²: 1.01 / Net I/σ(I): 5.6 / Num. measured all: 294769
Reflection shell	Resolution: 2.58→2.67 Å / % possible obs: 99.9 % / Redundancy: 6 % / R_merge(I) obs: 1.343 / Num. measured all: 27532 / Num. unique obs: 4579 / CC_1/2: 0.524 / R_pim(I) all: 0.6 / R_rim(I) all: 1.476 / Χ²: 0.98 / Net I/σ(I) obs: 1.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.58→107.2 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2451	2296	4.89 %
R_work	0.2099	-	-
obs	0.2116	46995	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.58→107.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10222	0	176	299	10697

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10677
X-RAY DIFFRACTION	f_angle_d	0.65	14456
X-RAY DIFFRACTION	f_dihedral_angle_d	13.075	3807
X-RAY DIFFRACTION	f_chiral_restr	0.044	1536
X-RAY DIFFRACTION	f_plane_restr	0.005	1843

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 (%)
2.58-2.64	0.3417	137	0.3122	2757	X-RAY DIFFRACTION	100
2.64-2.7	0.3277	135	0.2942	2773	X-RAY DIFFRACTION	100
2.7-2.76	0.3167	151	0.2774	2797	X-RAY DIFFRACTION	100
2.76-2.84	0.2875	137	0.2751	2785	X-RAY DIFFRACTION	100
2.84-2.92	0.2808	149	0.2695	2754	X-RAY DIFFRACTION	100
2.92-3.02	0.3205	148	0.261	2764	X-RAY DIFFRACTION	100
3.02-3.13	0.303	150	0.2654	2787	X-RAY DIFFRACTION	100
3.13-3.25	0.29	149	0.2504	2774	X-RAY DIFFRACTION	100
3.25-3.4	0.2567	151	0.2171	2768	X-RAY DIFFRACTION	100
3.4-3.58	0.2958	130	0.2209	2814	X-RAY DIFFRACTION	100
3.58-3.8	0.2212	153	0.1925	2790	X-RAY DIFFRACTION	100
3.8-4.1	0.2031	133	0.1752	2797	X-RAY DIFFRACTION	100
4.1-4.51	0.1906	171	0.1594	2769	X-RAY DIFFRACTION	100
4.51-5.16	0.1996	126	0.1572	2843	X-RAY DIFFRACTION	100
5.16-6.5	0.2252	123	0.2019	2836	X-RAY DIFFRACTION	100
6.5-107.2	0.2093	153	0.1743	2891	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	1.5755	0.4187	0.127	2.7301	-1.4335	2.5004	-0.0871	0.267	0.0479	-0.2471	0.0778	0.023	0.1145	0.0973	0.0232	0.2634	0.006	-0.0139	0.2528	-0.0404	0.2478	22.8161	6.306	36.2771
2	2.1001	-0.0727	0.0385	2.7874	-0.3087	4.6874	0.0483	-0.0874	-0.0325	-0.0742	-0.0038	0.5063	-0.2723	-0.269	0.1025	0.2363	-0.0072	0.0033	0.3077	-0.022	0.3125	19.8636	0.057	52.2171
3	3.2293	0.2908	0.0677	3.5512	-0.4898	2.861	0.0919	-0.1836	0.2159	0.2693	-0.1383	-0.1669	-0.2914	0.327	0.149	0.2378	0.0067	0.005	0.2724	0.0032	0.2961	32.8444	6.7892	56.8847
4	0.86	-0.4442	0.1532	4.4943	-0.775	1.8535	0.0142	0.0513	0.2031	0.1151	-0.0384	0.0142	-0.3865	0.0455	0.0233	0.2949	-0.0687	0.0301	0.3156	0.0263	0.2927	28.4946	23.7554	43.8825
5	2.8876	1.2354	0.3292	2.0112	-0.1454	2.4332	0.0145	0.7359	-0.317	-0.5808	0.2109	-0.3482	0.3398	0.5113	-0.2101	0.5286	0.0517	0.1486	0.5031	-0.1344	0.4673	63.7696	28.2267	22.793
6	0.7349	0.4929	1.252	4.1333	-0.5455	2.6245	0.0917	-0.5014	-0.0085	-0.0601	-0.076	-0.1073	0.3006	-0.0462	0.1504	0.3463	0.0332	0.0597	0.4775	-0.0423	0.394	61.8585	31.4459	35.9748
7	0.6671	0.2585	0.6557	1.4941	0.5313	2.2655	-0.0645	0.1487	-0.0766	-0.2439	0.0379	-0.074	0.0568	0.0004	0.016	0.3536	-0.0088	0.0788	0.2994	-0.0001	0.3494	53.3692	39.1899	33.1816
8	7.0009	2.1057	0.0332	1.8064	0.5729	1.7897	0.046	0.4153	-0.4434	-0.4672	0.1007	-0.0632	0.2711	-0.1196	-0.0973	0.6809	-0.002	-0.0258	0.3727	-0.0044	0.3899	35.8441	21.7728	18.3091
9	1.9375	1.5263	1.6172	2.4271	0.6275	1.6787	-0.2639	0.5416	0.1379	-0.4917	0.2898	-0.2133	-0.3773	0.593	-0.0123	0.5579	-0.0773	0.0971	0.4988	0.0025	0.3447	56.9201	41.8633	20.3976
10	5.8571	1.4811	-1.2465	0.8995	-1.2791	2.0425	-0.1739	0.7235	0.0584	-0.4448	0.0276	0.2525	0.374	0.0137	0.0482	0.6077	-0.0694	-0.03	0.4275	0.0259	0.2964	33.3381	25.2412	15.0327
11	2.8701	1.9057	0.7996	5.4175	1.1917	1.845	-0.2569	0.51	-0.2047	-0.1296	0.3204	-0.1277	-0.0582	-0.0917	-0.0638	0.5594	0.0087	0.0289	0.5272	-0.05	0.2907	47.8416	29.8558	14.8783
12	2.0234	-1.3422	-1.5762	4.5699	1.8159	2.4024	-0.3745	0.003	-0.0457	0.6253	0.1517	0.2268	0.4768	-0.3237	0.1346	0.5139	-0.043	-0.0441	0.4588	-0.0201	0.3196	12.9988	45.6412	18.0401
13	2.9424	-0.273	0.2539	2.7509	-0.1498	2.6579	0.0874	-0.268	-0.1422	0.3261	0.0572	-0.6439	0.2398	0.4127	-0.1138	0.3285	-0.0222	-0.02	0.2609	0.0082	0.3747	23.2124	42.4877	9.8017
14	2.2245	0.8833	-1.1228	0.7554	0.3426	6.3261	-0.0883	-0.0215	0.0557	0.1361	-0.1191	-0.2506	-0.1917	0.167	0.1002	0.3339	0.0312	0.0132	0.2773	0.0209	0.4119	17.8344	39.3831	-2.7051
15	1.368	0.4598	0.9212	1.2173	0.8084	2.8144	-0.0698	0.0326	0.119	-0.1708	-0.1215	0.1635	-0.1108	-0.2483	0.2443	0.3864	0.0296	0.0489	0.3597	-0.0477	0.3276	8.4026	47.5803	-1.8869
16	4.7484	-1.7402	0.267	2.8512	-0.4038	3.422	-0.2537	0.6605	1.616	-1.0129	-0.022	-1.023	-0.8547	0.2964	0.235	0.6458	-0.0546	0.0845	0.512	0.1177	0.6916	19.2017	74.1588	4.2727
17	2.1511	1.3164	-0.3486	6.1631	0.8967	2.7943	0.0745	0.1997	0.2474	0.2506	-0.0525	0.6296	-0.1953	-0.6058	0.0225	0.2713	0.05	0.0398	0.4528	-0.0664	0.3426	6.2561	57.0957	7.6454
18	1.9989	-1.1996	1.7101	2.2287	-2.5239	3.0616	-0.435	0.645	0.3331	0.2726	-0.0706	-0.4895	-1.5838	0.6647	0.5755	0.9342	-0.1014	0.0454	0.6005	0.0223	0.7436	17.3645	79.2905	6.9057
19	3.6131	2.3635	1.3104	4.859	2.442	3.591	-0.0184	-0.349	0.4783	0.0544	-0.2641	0.1771	-0.2	-0.275	0.3194	0.3465	0.0798	0.0195	0.27	-0.015	0.2389	11.622	60.8356	12.4322
20	1.785	-1.0741	-0.1705	2.1244	0.096	3.4112	0.0082	-0.2801	0.2411	0.7152	0.0407	0.2462	-0.2927	-0.0745	-0.0694	0.5105	-0.0375	0.0842	0.4519	-0.0149	0.3824	-18.3989	71.4516	40.5209
21	1.6716	-0.1674	-0.2765	1.5374	-0.6552	1.6061	0.0575	-0.2724	-0.2918	0.2271	0.107	0.4675	0.1304	-0.4657	-0.126	0.3334	-0.0194	0.0881	0.3194	0.0358	0.3541	-21.0447	64.5921	29.3505
22	1.8223	0.5004	0.5881	1.8996	-0.4855	2.8605	0.0209	0.0195	0.0055	0.1412	-0.0477	0.0452	0.0441	0.0954	0.0649	0.3665	0.026	0.0957	0.2674	0.0178	0.3121	-13.2394	76.1506	21.66
23	4.8751	2.1827	3.0445	1.6526	-0.1631	5.2999	-0.0466	0.6979	0.2597	-0.0795	0.2313	-0.028	0.1156	0.342	-0.3161	0.5594	-0.1034	0.0241	0.3514	-0.0187	0.5463	0.9354	84.3237	22.6481
24	1.3624	-0.1809	1.1952	1.1851	-0.4498	1.4301	-0.0519	-0.0808	-0.1674	0.1178	0.0846	0.1397	-0.1719	-0.0364	0.0652	0.3634	0.0137	0.1104	0.2922	0.0271	0.3395	-10.4501	76.013	25.7052
25	4.3592	-0.3715	-0.7423	0.9992	0.9286	1.9158	-0.002	-0.258	0.1843	0.5588	0.0126	-0.4756	0.0256	-0.069	0.0047	0.5411	0.0063	-0.0295	0.3231	0.0095	0.4182	9.145	60.2031	34.0272
26	2.6639	-0.7249	0.2837	2.0991	0.6498	1.1618	-0.0276	-0.5558	0.229	0.2227	0.1506	-0.2091	-0.2722	-0.125	-0.1864	0.5221	-0.0095	0.0443	0.362	-0.0376	0.2506	-2.5348	73.711	37.9436
27	6.8306	-1.0947	-3.425	1.9214	2.3483	3.556	-0.1362	-0.1722	-0.4116	0.635	-0.0388	-0.5356	0.1011	-0.6153	-0.0537	0.4579	0.0264	-0.1197	0.4907	-0.0321	0.4139	16.3734	59.977	33.0662
28	2.7458	-0.0988	-0.6992	4.4865	-0.1063	2.8492	-0.1486	-0.3756	0.213	0.4766	0.138	-0.3292	-0.511	0.1798	-0.0714	0.6034	0.0141	-0.0517	0.3994	-0.1041	0.3265	-2.2312	81.9064	39.0101
29	3.7785	1.0739	0.4935	9.2208	1.6613	3.1557	-0.0709	-0.2393	-0.2749	1.022	0.2381	0.4433	0.4544	0.2135	-0.0518	0.4962	0.0572	0.0868	0.4582	0.1543	0.4454	-1.7898	54.7922	41.0311

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 81 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 132 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 133 through 191 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 192 through 344 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 9 through 81 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 82 through 111 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 112 through 216 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 217 through 246 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 247 through 268 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 269 through 304 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 305 through 343 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 8 through 37 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 38 through 89 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 90 through 132 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 133 through 216 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 217 through 240 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 241 through 284 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 285 through 304 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 305 through 344 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 10 through 37 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 38 through 89 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 90 through 156 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 157 through 171 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 172 through 216 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 217 through 246 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 247 through 287 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 288 through 304 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 305 through 323 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 324 through 344 )

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