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- PDB-8qnc: Crystal structure of ancestral L-galactono-1,4-lactone dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 8qnc
TitleCrystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: A113G variant
ComponentsL-galactono-1,4-lactone dehydrogenase: A113G variant
KeywordsFLAVOPROTEIN / biocatalysis / Vitamin C
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBoverio, A. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Not funded Italy
CitationJournal: Nat Commun / Year: 2024
Title: Structure, mechanism, and evolution of the last step in vitamin C biosynthesis.
Authors: Boverio, A. / Jamil, N. / Mannucci, B. / Mascotti, M.L. / Fraaije, M.W. / Mattevi, A.
History
DepositionSep 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-galactono-1,4-lactone dehydrogenase: A113G variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3175
Polymers57,2411
Non-polymers1,0764
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-5 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.387, 69.657, 67.608
Angle α, β, γ (deg.)90.00, 98.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein L-galactono-1,4-lactone dehydrogenase: A113G variant


Mass: 57240.945 Da / Num. of mol.: 1 / Mutation: A113G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: L-galactonolactone dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M Lithium Nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.7→66.9 Å / Num. obs: 53389 / % possible obs: 98.9 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.043 / Rrim(I) all: 0.102 / Χ2: 1.02 / Net I/σ(I): 10.7 / Num. measured all: 292668
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 1.336 / Num. measured all: 15649 / Num. unique obs: 2825 / CC1/2: 0.593 / Rpim(I) all: 0.618 / Rrim(I) all: 1.477 / Χ2: 1.05 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→66.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.473 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21192 2623 4.9 %RANDOM
Rwork0.17874 ---
obs0.18036 50741 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.772 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-1.31 Å2
2--0.24 Å2-0 Å2
3---0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.7→66.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3823 0 72 295 4190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133998
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173758
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.655433
X-RAY DIFFRACTIONr_angle_other_deg1.4011.5788695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74822.404208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81915679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4741528
X-RAY DIFFRACTIONr_chiral_restr0.0830.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02860
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4982.4681949
X-RAY DIFFRACTIONr_mcbond_other2.4992.4681948
X-RAY DIFFRACTIONr_mcangle_it3.6893.6882435
X-RAY DIFFRACTIONr_mcangle_other3.6883.6882436
X-RAY DIFFRACTIONr_scbond_it3.562.8642049
X-RAY DIFFRACTIONr_scbond_other3.562.8642050
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4474.1262998
X-RAY DIFFRACTIONr_long_range_B_refined6.96129.3134460
X-RAY DIFFRACTIONr_long_range_B_other6.94129.0694410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 214 -
Rwork0.367 3714 -
obs--99.24 %

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