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- PDB-7svq: Crystal Structure of L-galactose dehydrogenase from Spinacia oler... -

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Basic information

Entry
Database: PDB / ID: 7svq
TitleCrystal Structure of L-galactose dehydrogenase from Spinacia oleracea in complex with NAD+
ComponentsL-galactose dehydrogenase
KeywordsPLANT PROTEIN / L-galactose dehydrogenase Enzyme
Function / homology
Function and homology information


L-galactose dehydrogenase activity / L-ascorbic acid biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
L-galactose dehydrogenase-like / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-galactose dehydrogenase
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSantillan, J.A.V. / Cabrejos, D.A.L. / Pereira, H.M. / Gomez, J.C.C. / Garratt, R.C.
Funding support Peru, 2items
OrganizationGrant numberCountry
Other government188-2018-INIA-PNIA-PASANTIA Peru
Other government069-2019-FONDECYT Peru
CitationJournal: Plant Cell.Physiol. / Year: 2022
Title: Structural Characterization of L-Galactose Dehydrogenase: An Essential Enzyme for Vitamin C Biosynthesis.
Authors: Vargas, J.A. / Leonardo, D.A. / D'Muniz Pereira, H. / Lopes, A.R. / Rodriguez, H.N. / Cobos, M. / Marapara, J.L. / Castro, J.C. / Garratt, R.C.
History
DepositionNov 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-galactose dehydrogenase
B: L-galactose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5284
Polymers75,2012
Non-polymers1,3272
Water9,548530
1
A: L-galactose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2642
Polymers37,6001
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L-galactose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2642
Polymers37,6001
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.020, 54.980, 63.241
Angle α, β, γ (deg.)86.820, 69.120, 84.140
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 33 or resid 35...
21(chain B and (resid 6 through 33 or resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPHEPHE(chain A and (resid 6 through 33 or resid 35...AA6 - 3327 - 54
12ASPASPASPASP(chain A and (resid 6 through 33 or resid 35...AA35 - 18056 - 201
13VALVALLYSLYS(chain A and (resid 6 through 33 or resid 35...AA182 - 247203 - 268
14LYSLYSLYSLYS(chain A and (resid 6 through 33 or resid 35...AA248269
15LYSLYSNADNAD(chain A and (resid 6 through 33 or resid 35...AA - C6 - 40127
16LYSLYSNADNAD(chain A and (resid 6 through 33 or resid 35...AA - C6 - 40127
17LYSLYSNADNAD(chain A and (resid 6 through 33 or resid 35...AA - C6 - 40127
18LYSLYSNADNAD(chain A and (resid 6 through 33 or resid 35...AA - C6 - 40127
21LYSLYSPHEPHE(chain B and (resid 6 through 33 or resid 35...BB6 - 3327 - 54
22ASPASPASPASP(chain B and (resid 6 through 33 or resid 35...BB35 - 18056 - 201
23VALVALLEULEU(chain B and (resid 6 through 33 or resid 35...BB182 - 271203 - 292
24GLYGLYNADNAD(chain B and (resid 6 through 33 or resid 35...BB - D273 - 401294

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Components

#1: Protein L-galactose dehydrogenase


Mass: 37600.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: GDH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): DE3 / References: UniProt: Q6BDJ2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.75→39.73 Å / Num. obs: 55241 / % possible obs: 87.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.07 Å2 / CC1/2: 0.958 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.069 / Rrim(I) all: 0.128 / Net I/σ(I): 7.5 / Num. measured all: 190355 / Scaling rejects: 692
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.75-1.783.30.595464514160.7060.3810.7091.840.8
9.09-39.733.80.03616544410.9930.0230.04318.997.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SMI

7smi


Resolution: 1.75→34 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 2756 5.01 %
Rwork0.182 52210 -
obs0.1837 54966 87.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.74 Å2 / Biso mean: 18.5718 Å2 / Biso min: 6.34 Å2
Refinement stepCycle: final / Resolution: 1.75→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 88 530 5450
Biso mean--15.87 25.85 -
Num. residues----630
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2948X-RAY DIFFRACTION5.901TORSIONAL
12B2948X-RAY DIFFRACTION5.901TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.780.36620.28011212127440
1.78-1.810.335720.25331437150948
1.81-1.850.2849890.23661654174355
1.85-1.890.2571130.22731923203666
1.89-1.930.30291200.23742444256481
1.93-1.970.23221490.20862803295293
1.97-2.020.22851620.20042831299395
2.02-2.070.25351350.20272870300596
2.07-2.140.19991240.18292919304396
2.14-2.20.23491350.17722918305396
2.2-2.280.21621390.18472898303796
2.28-2.370.22571580.1792898305697
2.38-2.480.23061230.18222913303697
2.48-2.610.23171540.18692962311697
2.61-2.780.22371590.19172883304297
2.78-2.990.23741600.19562920308098
2.99-3.290.22231730.18622922309598
3.29-3.770.20121770.16682909308698
3.77-4.750.13731780.1412948312699
4.75-340.2011740.162946312099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.19260.32691.03672.5724-2.31472.9417-0.1489-0.24690.20030.2810.1675-0.0138-0.4057-0.61690.01510.15610.040.01440.1679-0.03350.1725-8.029135.2801-0.262
22.70140.946-0.64121.8294-1.03153.15710.0089-0.0252-0.8166-0.08250.0439-0.67450.80430.63290.01610.2790.103-0.03080.21160.00140.3511-1.243413.79821.2629
31.7889-0.1605-1.23020.740.53312.4059-0.0199-0.0731-0.10880.1230.01330.05770.1852-0.09720.03190.0898-0.005-0.00570.06460.0220.1099-8.329217.5493-4.0141
41.6425-0.0341-0.26941.56780.04841.03830.02930.1348-0.0069-0.1318-0.04840.0454-0.0279-0.03160.02340.09670.0232-0.00880.07680.00520.0991-3.779125.1743-18.1458
52.2439-0.69521.28332.655-0.86962.2146-0.0501-0.01680.10530.05020.04430.0453-0.0902-0.0070.0250.08550.00210.02850.0937-0.01270.09767.388530.7805-3.9041
62.72860.2807-0.02882.26690.66744.33850.0028-0.1876-0.16110.2995-0.0223-0.21510.42450.18880.00060.12830.0172-0.00670.1050.01590.113817.311218.69566.5683
72.58020.06091.33032.256-0.19212.40360.0002-0.29260.16270.1846-0.07120.1122-0.0450.05810.0480.09610.00490.04720.1467-0.00980.09844.390828.67637.2516
82.87983.28511.4989.80164.64413.33170.05-0.3099-0.03460.4265-0.1936-0.06210.164-0.06180.07840.14550.01220.01050.2091-0.01320.0975-1.751527.182913.4817
92.15840.16270.63020.8999-0.69710.82130.0856-0.37730.15560.2163-0.0298-0.0935-0.08060.0039-0.04350.0809-0.00480.00710.1482-0.02690.1616.95229.64413.5924
101.97410.36330.08610.58660.94972.9622-0.03910.17490.1058-0.21680.06920.0416-0.20150.0664-0.06550.06480.0431-0.00660.09970.03610.110321.3421-4.1073-28.8998
113.86960.7796-2.28932.2864-0.25475.63110.02420.3063-0.1113-0.0343-0.0055-0.05560.1241-0.0135-0.00360.02680.0277-0.03830.1069-0.00330.094823.0659-12.3372-29.309
121.883-0.3437-0.23381.03920.36770.7802-0.0162-0.0224-0.02830.0711-0.0031-0.04940.00550.0130.0350.07320.0008-0.00610.05810.01150.078119.5542-6.4429-13.4012
131.97630.63940.94673.03561.26381.7767-0.06990.09540.1551-0.08950.0856-0.0198-0.1350.0285-0.03170.09290.01120.0310.09070.01110.09739.57782.7971-25.7927
142.9625-1.0423-0.79722.2543-0.1815.8023-0.09680.406-0.135-0.23020.07580.08850.1519-0.18430.01660.0761-0.0492-0.02110.1679-0.00960.1189-0.4521-8.9337-36.4387
152.4054-0.06590.77892.5080.05572.96550.0080.2280.1333-0.17370.066-0.0254-0.3319-0.1404-0.03460.090.00040.03860.16640.02520.105113.2229-0.0933-36.5687
164.0349-2.13560.83813.1791-3.2544.08610.05210.55450.1515-0.5522-0.2028-0.35530.10120.21060.03250.1221-0.01090.02670.26630.00510.108919.5531-2.2948-42.2448
172.2295-0.5732-0.11921.2940.64073.06290.12350.45940.3239-0.263-0.08220.0972-0.4304-0.1071-0.01230.14410.0105-0.0230.19790.05760.20030.32882.3341-34.2417
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 21 )A6 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 37 )A22 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 101 )A38 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 180 )A102 - 180
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 222 )A181 - 222
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 248 )A223 - 248
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 276 )A249 - 276
8X-RAY DIFFRACTION8chain 'A' and (resid 277 through 293 )A277 - 293
9X-RAY DIFFRACTION9chain 'A' and (resid 294 through 320 )A294 - 320
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 37 )B6 - 37
11X-RAY DIFFRACTION11chain 'B' and (resid 38 through 65 )B38 - 65
12X-RAY DIFFRACTION12chain 'B' and (resid 66 through 180 )B66 - 180
13X-RAY DIFFRACTION13chain 'B' and (resid 181 through 222 )B181 - 222
14X-RAY DIFFRACTION14chain 'B' and (resid 223 through 248 )B223 - 248
15X-RAY DIFFRACTION15chain 'B' and (resid 249 through 276 )B249 - 276
16X-RAY DIFFRACTION16chain 'B' and (resid 277 through 293 )B277 - 293
17X-RAY DIFFRACTION17chain 'B' and (resid 294 through 320 )B294 - 320

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