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

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Basic information

Entry
Database: PDB / ID: 8qnb
TitleCrystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: in complex with L-galactono-1,4-lactone
ComponentsL-galactono-1,4-lactone dehydrogenase
KeywordsFLAVOPROTEIN / Oxidoreductases / Anestral enzyme
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBoverio, A. / Mattevi, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2193
Polymers57,2551
Non-polymers9642
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-10 kcal/mol
Surface area19540 Å2
Unit cell
Length a, b, c (Å)57.527, 69.964, 71.239
Angle α, β, γ (deg.)90.00, 103.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 57254.969 Da / Num. of mol.: 1
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 / Comment: FAD*YM
#3: Chemical ChemComp-X8X / L-galactono-1,4-lactone / (3S,4S,5R)-5-[(1S)-1,2-bis(oxidanyl)ethyl]-3,4-bis(oxidanyl)oxolan-2-one / gamma-L-galactonolactone


Mass: 178.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 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: Feb 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.1→49.25 Å / Num. obs: 31671 / % possible obs: 98.4 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.031 / Rrim(I) all: 0.101 / Χ2: 1.02 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 99 % / Redundancy: 10.1 % / Rmerge(I) obs: 1.891 / Num. measured all: 26455 / Num. unique obs: 2611 / CC1/2: 0.787 / Rpim(I) all: 0.62 / Rrim(I) all: 1.992 / Χ2: 1.02 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.986 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25433 1570 5 %RANDOM
Rwork0.19959 ---
obs0.20225 30085 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.393 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å20 Å2-5.64 Å2
2--0.57 Å2-0 Å2
3----1.14 Å2
Refinement stepCycle: 1 / Resolution: 2.1→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3754 0 65 131 3950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133931
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173674
X-RAY DIFFRACTIONr_angle_refined_deg1.491.655349
X-RAY DIFFRACTIONr_angle_other_deg1.2451.5778498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1345481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57822.367207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27115665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5191528
X-RAY DIFFRACTIONr_chiral_restr0.190.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024406
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02855
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_it3.3214.7391915
X-RAY DIFFRACTIONr_mcbond_other3.3214.7381914
X-RAY DIFFRACTIONr_mcangle_it4.9167.0962390
X-RAY DIFFRACTIONr_mcangle_other4.9157.0972391
X-RAY DIFFRACTIONr_scbond_it3.8775.1252016
X-RAY DIFFRACTIONr_scbond_other3.8765.1252017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9117.5082957
X-RAY DIFFRACTIONr_long_range_B_refined7.78354.2914283
X-RAY DIFFRACTIONr_long_range_B_other7.78254.2724276
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 109 -
Rwork0.346 2224 -
obs--98.77 %

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