PDB-8sg0: Crystal Structure of GDP-manose 3,5 epimerase de Myrciaria dubia ...

ID or keywords:

Entry

Database: PDB / ID: 8sg0

Title

Crystal Structure of GDP-manose 3,5 epimerase de Myrciaria dubia in complex with substrate, product and NAD

Components

GDP-mannose 3,5-epimerase

Keywords

PLANT PROTEIN / L-galactose 1-dehydrogenase / Enzyme

Function / homology

GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Function and homology information

Biological species

Myrciaria dubia (camu-camu)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.25 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 11, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8sg0.cif.gz	322.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8sg0.ent.gz	255.5 KB	Display	PDB format
PDBx/mmJSON format	8sg0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8sg0_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	8sg0_full_validation.pdf.gz	2.9 MB	Display
Data in XML	8sg0_validation.xml.gz	40.7 KB	Display
Data in CIF	8sg0_validation.cif.gz	62.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sg/8sg0 ftp://data.pdbj.org/pub/pdb/validation_reports/sg/8sg0	HTTPS FTP

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Related structure data

Related structure data	7smlC 8sccC 8skbC 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

hetero molecules

96.9 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, light scattering

Unit cell

Length a, b, c (Å)	89.799, 60.839, 133.999
Angle α, β, γ (deg.)	90.00, 105.86, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-876- HOH
2	1	B-881- HOH
3	1	B-968- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	GDP-mannose 3,5-epimerase Mass: 46500.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myrciaria dubia (camu-camu) / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: GDP-mannose 3,5-epimerase

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Non-polymers , 5 types, 1090 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₂₅N₅O₁₆P₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GDC / GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₂₅N₅O₁₆P₂ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1082 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 1.89 Å³/Da / Density % sol: 35.38 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Lithium sulfate, 0.1 M Tris 8.5, 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: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 25, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.25→44.81 Å / Num. obs: 184491 / % possible obs: 96.3 % / Redundancy: 6.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.065 / R_pim(I) all: 0.028 / R_rim(I) all: 0.071 / Χ²: 0.89 / Net I/σ(I): 14 / Num. measured all: 1145495
Reflection shell	Resolution: 1.25→1.27 Å / % possible obs: 67.4 % / Redundancy: 3.5 % / R_merge(I) obs: 0.41 / Num. measured all: 22357 / Num. unique obs: 6305 / CC_1/2: 0.831 / R_pim(I) all: 0.244 / R_rim(I) all: 0.48 / Χ²: 0.81 / Net I/σ(I) obs: 2.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
GDA		data collection
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.25→44.81 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1639	9383	5.09 %
R_work	0.1502	-	-
obs	0.1509	184474	96.22 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.25→44.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5713	0	254	1087	7054

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	6176
X-RAY DIFFRACTION	f_angle_d	0.99	8392
X-RAY DIFFRACTION	f_dihedral_angle_d	12.654	2219
X-RAY DIFFRACTION	f_chiral_restr	0.083	892
X-RAY DIFFRACTION	f_plane_restr	0.007	1045

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 (%)
1.25-1.26	0.2278	214	0.2124	3931	X-RAY DIFFRACTION	65
1.26-1.28	0.2332	249	0.2032	4375	X-RAY DIFFRACTION	73
1.28-1.29	0.2175	250	0.2004	4734	X-RAY DIFFRACTION	78
1.29-1.31	0.1971	281	0.1922	5185	X-RAY DIFFRACTION	86
1.31-1.33	0.1944	282	0.1913	5538	X-RAY DIFFRACTION	91
1.33-1.35	0.1934	324	0.1817	5697	X-RAY DIFFRACTION	95
1.35-1.37	0.1933	309	0.1773	5963	X-RAY DIFFRACTION	99
1.37-1.39	0.2015	351	0.1725	6031	X-RAY DIFFRACTION	99
1.39-1.41	0.1691	290	0.1645	6024	X-RAY DIFFRACTION	100
1.41-1.43	0.1927	363	0.1665	6037	X-RAY DIFFRACTION	100
1.43-1.46	0.1679	325	0.1653	6040	X-RAY DIFFRACTION	100
1.46-1.48	0.1716	318	0.1584	6024	X-RAY DIFFRACTION	100
1.48-1.51	0.1703	316	0.1512	6073	X-RAY DIFFRACTION	100
1.51-1.54	0.1665	341	0.1478	6035	X-RAY DIFFRACTION	100
1.54-1.57	0.1666	297	0.1455	6036	X-RAY DIFFRACTION	100
1.57-1.61	0.1592	320	0.144	6047	X-RAY DIFFRACTION	100
1.61-1.65	0.1586	347	0.1442	6063	X-RAY DIFFRACTION	100
1.65-1.7	0.1702	313	0.1464	6100	X-RAY DIFFRACTION	100
1.7-1.75	0.1665	313	0.1489	6049	X-RAY DIFFRACTION	100
1.75-1.8	0.1668	319	0.1498	6052	X-RAY DIFFRACTION	100
1.8-1.87	0.1587	313	0.1499	6124	X-RAY DIFFRACTION	100
1.87-1.94	0.153	324	0.1437	6034	X-RAY DIFFRACTION	100
1.94-2.03	0.1573	351	0.1448	6026	X-RAY DIFFRACTION	100
2.03-2.14	0.1602	354	0.1397	6033	X-RAY DIFFRACTION	100
2.14-2.27	0.1649	311	0.142	6118	X-RAY DIFFRACTION	100
2.27-2.45	0.163	330	0.1492	6083	X-RAY DIFFRACTION	100
2.45-2.69	0.1448	335	0.1496	6080	X-RAY DIFFRACTION	100
2.69-3.08	0.1544	326	0.1521	6109	X-RAY DIFFRACTION	100
3.08-3.88	0.1496	302	0.137	6191	X-RAY DIFFRACTION	100
3.88-44.81	0.1574	315	0.1388	6259	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	2.1383	-0.6174	-1.8958	1.7045	1.0575	2.3286	-0.0815	0.0232	-0.05	-0.0815	0.0162	-0.0324	0.061	0.056	0.059	0.0704	-0.0024	-0.0194	0.0825	0.0118	0.0152	18.8627	-6.4102	3.462
2	0.3628	0.0987	-0.3015	0.7319	0.2678	0.9972	-0.0013	0.0833	0.0377	-0.0669	0.0354	0.0639	-0.0552	-0.1047	-0.0283	0.0617	0.007	-0.0092	0.0931	0.0101	0.0778	7.786	0.799	13.0333
3	0.2596	0.1062	-0.1139	0.4318	-0.1104	0.3073	0.0001	-0.0038	-0.005	0.0194	-0.0035	-0.0118	-0.0224	0.01	0.0033	0.059	-0.0016	-0.0011	0.0638	-0.002	0.0564	19.14	-1.975	24.3504
4	0.3473	-0.1654	0.0514	1.1348	0.0336	0.4797	-0.0255	-0.0091	0.0581	0.059	0.002	-0.0551	-0.0938	0.0076	0.0208	0.0562	-0.0062	-0.0002	0.0616	0.0015	0.0447	26.4528	14.5779	18.9581
5	0.4955	-0.4138	0.1321	1.738	-0.3255	0.868	0.0289	0.0768	0.0217	-0.0874	-0.0389	0.0014	-0.0755	-0.0283	0.002	0.0658	-0.0115	0.0031	0.076	-0.0022	0.0473	23.5392	13.9258	9.5373
6	0.1384	0.2433	-0.0478	0.3807	-0.0784	0.0112	0.0611	-0.0029	0.0567	0.148	-0.0218	0.3055	-0.0907	-0.1643	-0.0611	0.1845	0.02	0.0315	0.1922	-0.0024	0.2163	6.0779	17.5296	24.7607
7	1.0719	-0.0257	0.1145	1.0338	0.1407	2.0541	0.0427	-0.1835	-0.0736	0.1603	0.0069	0.0168	0.1924	-0.1288	-0.0457	0.0699	-0.0016	-0.0006	0.0889	0.0055	0.0676	-0.7041	-16.478	52.8138
8	0.3529	-0.045	-0.0095	0.4108	-0.0626	0.3708	-0.0044	-0.0162	-0.0443	0.0197	-0.0071	-0.033	0.039	0.0134	0.0147	0.0533	-0.0024	0.0034	0.0595	-0.0043	0.0648	15.2258	-19.5982	46.9675

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 111 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 112 through 216 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 217 through 309 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 310 through 345 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 346 through 370 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 11 through 81 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 82 through 370 )

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