PDB-8scc: Crystal Structure of L-galactose 1-dehydrogenase de Myrciaria dubia

ID or keywords:

Entry

Database: PDB / ID: 8scc

Title

Crystal Structure of L-galactose 1-dehydrogenase de Myrciaria dubia

Components

L-galactose dehydrogenase

Keywords

PLANT PROTEIN / L-galactose 1-dehydrogenase / Enzyme

Biological species

Myrciaria dubia (camu-camu)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 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 5, 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	8scc.cif.gz	249.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8scc.ent.gz	200.4 KB	Display	PDB format
PDBx/mmJSON format	8scc.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/sc/8scc ftp://data.pdbj.org/pub/pdb/validation_reports/sc/8scc	HTTPS FTP

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Related structure data

Related structure data	7smlC 8sg0C 8skbC 8usuC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: L-galactose dehydrogenase

B: L-galactose dehydrogenase

78.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: L-galactose dehydrogenase

defined by author&software
Evidence: gel filtration
39.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: L-galactose dehydrogenase

defined by software
39.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.310, 55.796, 107.732
Angle α, β, γ (deg.)	90.00, 110.00, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-601- HOH

#1: Protein	L-galactose dehydrogenase Mass: 39347.012 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: EC: 1.1.1.316
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.25 Å³/Da / Density % sol: 45.3 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.5M Ammonium sulfate, 1.0M Lithium sulfate, 0.1M Sodium citrate

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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: Sep 28, 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: 2.09→101.23 Å / Num. obs: 41096 / % possible obs: 98 % / Redundancy: 4.1 % / CC_1/2: 0.982 / R_merge(I) obs: 0.239 / R_pim(I) all: 0.131 / R_rim(I) all: 0.273 / Χ²: 0.95 / Net I/σ(I): 6.3 / Num. measured all: 168734
Reflection shell	Resolution: 2.09→2.2 Å / % possible obs: 87.1 % / Redundancy: 3.9 % / R_merge(I) obs: 0.912 / Num. measured all: 20450 / Num. unique obs: 5282 / CC_1/2: 0.662 / R_pim(I) all: 0.511 / R_rim(I) all: 1.049 / Χ²: 0.88 / Net I/σ(I) obs: 2.5

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
Aimless		data scaling
autoPROC		data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.09→101.23 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2187	2034	4.96 %	Randon selection
R_work	0.1804	-	-	-
obs	0.1823	41028	97.75 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.09→101.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4651	0	0	369	5020

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4735
X-RAY DIFFRACTION	f_angle_d	0.856	6408
X-RAY DIFFRACTION	f_dihedral_angle_d	11.789	1762
X-RAY DIFFRACTION	f_chiral_restr	0.054	737
X-RAY DIFFRACTION	f_plane_restr	0.008	826

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 (%)
2.09-2.13	0.2707	114	0.2192	1877	X-RAY DIFFRACTION	71
2.13-2.19	0.2441	150	0.2094	2566	X-RAY DIFFRACTION	99
2.19-2.25	0.2661	138	0.2147	2641	X-RAY DIFFRACTION	99
2.25-2.31	0.2538	131	0.2038	2633	X-RAY DIFFRACTION	100
2.31-2.39	0.2789	135	0.2036	2641	X-RAY DIFFRACTION	100
2.39-2.47	0.2684	106	0.1971	2637	X-RAY DIFFRACTION	100
2.47-2.57	0.2413	128	0.1849	2668	X-RAY DIFFRACTION	100
2.57-2.69	0.2246	146	0.1884	2645	X-RAY DIFFRACTION	100
2.69-2.83	0.2734	138	0.1866	2640	X-RAY DIFFRACTION	100
2.83-3.01	0.2163	142	0.1852	2640	X-RAY DIFFRACTION	100
3.01-3.24	0.2075	167	0.1887	2629	X-RAY DIFFRACTION	100
3.24-3.57	0.2315	118	0.1793	2673	X-RAY DIFFRACTION	100
3.57-4.08	0.1806	127	0.1502	2665	X-RAY DIFFRACTION	99
4.08-5.14	0.1658	150	0.1412	2691	X-RAY DIFFRACTION	100
5.14-101.23	0.189	144	0.1826	2748	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	1.309	-0.5156	0.0616	1.0333	0.7413	1.7014	0.1461	0.056	0.1576	-0.0977	-0.0601	0.0035	0.1142	-0.0438	-0.0558	0.1189	0.0073	-0.0129	0.1191	0.0176	0.1608	30.8607	1.2925	40.4
2	1.3418	0.4304	-0.5696	1.7756	-0.3397	1.5721	-0.0283	-0.0319	-0.1208	-0.1262	0.0409	-0.0613	0.1248	0.0704	-0.0281	0.0965	0.0061	-0.0075	0.1472	0.0054	0.1346	34.1265	-7.7529	38.6454
3	4.7158	0.9543	-1.8827	1.3011	-0.3905	2.69	-0.1959	0.2916	-0.5936	0.0865	0.0837	-0.0426	0.3341	-0.1445	0.1313	0.134	-0.0019	0.0183	0.1389	-0.0364	0.1985	32.6422	-13.1994	45.362
4	0.7785	-0.0649	-0.0398	0.7116	-0.0637	0.4325	-0.0014	-0.0637	-0.0092	0.025	-0.0006	-0.0291	-0.018	0.0088	0.0038	0.0637	-0.0016	-0.0113	0.0962	-0.0055	0.1006	22.4294	0.9301	51.3525
5	2.0923	0.6121	-1.0699	2.5644	-2.7937	3.4353	-0.1457	0.2593	-0.2151	-0.759	-0.0424	0.1259	0.667	-0.3467	0.1551	0.3174	-0.0289	-0.0692	0.1888	-0.0079	0.1829	7.9436	-4.5487	27.4169
6	0.9148	-0.4029	0.1866	0.3671	-0.4278	1.8756	0.0318	0.1224	-0.0535	-0.3436	-0.2044	-0.2423	0.1678	0.1132	0.1517	0.2362	0.0098	0.062	0.1691	0.0197	0.1331	23.1609	3.172	30.9989
7	1.1019	-0.3467	0.0102	0.9289	-0.0439	0.4292	0.0489	0.1962	-0.025	-0.2442	-0.0581	0.1022	-0.1301	-0.1046	0.0023	0.2266	0.0183	-0.0316	0.1607	0.0002	0.1396	17.623	3.9898	28.1527
8	1.6682	-0.1264	-0.5092	1.5232	0.4077	2.1612	0.0471	-0.0783	-0.1156	0.2397	-0.141	-0.2916	0.0453	0.1215	0.0432	0.1916	0.0031	-0.0378	0.1788	0.0136	0.2425	42.1106	-34.4442	19.1809
9	2.8525	0.0738	-0.9369	1.2959	0.3095	2.7443	0.4282	-0.1234	0.5444	0.2828	-0.0562	-0.0123	-1.4718	0.334	-0.2012	0.6085	-0.1444	0.0783	0.3273	-0.0766	0.3139	41.2512	-16.4064	24.2911
10	1.2849	0.0835	-0.1429	1.2023	-0.3952	2.3942	0.0629	-0.1609	0.2685	0.0983	-0.086	-0.2347	-0.9212	0.2943	0.0625	0.384	-0.0774	-0.0149	0.2401	-0.0107	0.1959	43.3046	-17.6818	14.9643
11	1.2488	-0.0678	0.0301	1.4201	0.0932	1.6769	-0.0884	0.0255	0.0066	-0.408	-0.0904	-0.3845	-0.1821	0.2679	0.1476	0.2637	-0.0391	0.0646	0.1788	0.0136	0.2233	44.4283	-22.2917	3.5933
12	1.0438	0.698	-0.4474	1.016	-0.4349	1.0273	-0.0772	0.0683	-0.1517	-0.0678	0.0166	-0.1284	0.1281	0.0465	0.0915	0.2606	0.0249	0.0485	0.1537	-0.0016	0.1643	35.8851	-33.7681	5.907
13	1.427	0.3666	-0.0592	1.8105	-0.8564	3.2032	0.2252	0.1163	0.3422	0.2821	0.1041	0.5192	-0.5025	-0.5215	-0.2984	0.2411	0.035	0.0752	0.1823	0.0184	0.2678	14.395	-23.608	17.178
14	1.8463	-0.0092	-0.9866	1.431	0.5855	1.5126	0.1715	-0.1837	0.089	0.2836	-0.0813	-0.1259	-0.0159	0.0352	-0.1051	0.274	0.0232	0.0283	0.1917	0.0229	0.1148	29.1975	-30.903	22.1908
15	3.1555	1.031	-0.1137	4.3994	0.0721	2.5686	-0.07	-0.5789	0.225	0.29	0.1963	0.0988	-0.4132	-0.1128	-0.217	0.3536	0.0068	-0.0262	0.2999	-0.0204	0.1762	32.4062	-27.3691	29.415
16	1.2153	-0.1395	-0.3778	1.6048	-0.5272	1.2701	-0.021	0.0399	-0.1353	0.0277	0.1689	0.2903	0.3382	-0.0851	0.0794	0.2041	0.0089	0.0174	0.1617	-0.0019	0.1868	17.5668	-33.8945	17.0027

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 80 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 81 through 224 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 225 through 251 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 252 through 278 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 279 through 321 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 9 through 27 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 28 through 53 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 54 through 80 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 81 through 142 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 143 through 224 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 225 through 251 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 252 through 278 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 279 through 294 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 295 through 322 )

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