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- PDB-8qmy: Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 8qmy
TitleCrystal structure of ancestral L-galactono-1,4-lactone dehydrogenase
Componentsancestral L-galactono-1,4-lactone dehydrogenase
KeywordsFLAVOPROTEIN / Vitamin C / carbohydrate oxidase
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 25, 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

Downloads & links

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Assembly

Deposited unit
A: ancestral L-galactono-1,4-lactone dehydrogenase
B: ancestral L-galactono-1,4-lactone dehydrogenase
C: ancestral L-galactono-1,4-lactone dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,24118
Polymers171,7653
Non-polymers3,47615
Water9,890549
1
A: ancestral L-galactono-1,4-lactone dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3175
Polymers57,2551
Non-polymers1,0624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ancestral L-galactono-1,4-lactone dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6078
Polymers57,2551
Non-polymers1,3527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ancestral L-galactono-1,4-lactone dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3175
Polymers57,2551
Non-polymers1,0624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.047, 98.016, 238.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein ancestral L-galactono-1,4-lactone dehydrogenase


Mass: 57254.969 Da / Num. of mol.: 3
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.: 3 / 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.: 11 / 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.: 549 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
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 X 4M / Detector: PIXEL / Date: Feb 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.9→48.05 Å / Num. obs: 126385 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Χ2: 1.07 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.93 Å / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.734 / Num. measured all: 42710 / Num. unique obs: 6164 / CC1/2: 0.562 / Rpim(I) all: 0.702 / Rrim(I) all: 1.873 / Χ2: 1.06 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.445 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23241 6184 4.9 %RANDOM
Rwork0.19472 ---
obs0.19655 120091 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.841 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--2.08 Å2-0 Å2
3----2.95 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11163 0 232 549 11944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01311788
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711116
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.6516000
X-RAY DIFFRACTIONr_angle_other_deg1.3151.57925686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88151425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79622.188617
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.955151989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0841586
X-RAY DIFFRACTIONr_chiral_restr0.0670.21496
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022558
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_it3.334.0815730
X-RAY DIFFRACTIONr_mcbond_other3.3274.085729
X-RAY DIFFRACTIONr_mcangle_it4.6116.1027145
X-RAY DIFFRACTIONr_mcangle_other4.6126.1037146
X-RAY DIFFRACTIONr_scbond_it4.0474.5256058
X-RAY DIFFRACTIONr_scbond_other4.0464.5256059
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9576.5978856
X-RAY DIFFRACTIONr_long_range_B_refined7.59347.13412974
X-RAY DIFFRACTIONr_long_range_B_other7.57647.03212900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A15411
12B15411
21A15386
22C15386
31B15449
32C15449
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 446 -
Rwork0.354 8783 -
obs--99.85 %

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