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- PDB-8ot8: Alditol oxidase from Actinomycetota bacterium in complex with D-x... -

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Basic information

Entry
Database: PDB / ID: 8ot8
TitleAlditol oxidase from Actinomycetota bacterium in complex with D-xylulose
ComponentsFAD-binding protein
KeywordsFLAVOPROTEIN / Alditol oxidase / xylulose
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / D-XYLULOSE / :
Function and homology information
Biological speciesActinomycetota bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRotilio, L. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione CARIPLO2020-0894 Italy
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2024
Title: Discovery and biochemical characterization of thermostable glycerol oxidases.
Authors: Santema, L.L. / Rotilio, L. / Xiang, R. / Tjallinks, G. / Guallar, V. / Mattevi, A. / Fraaije, M.W.
History
DepositionApr 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD-binding protein
B: FAD-binding protein
C: FAD-binding protein
D: FAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,44712
Polymers184,7044
Non-polymers3,7438
Water79344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-28 kcal/mol
Surface area57350 Å2
Unit cell
Length a, b, c (Å)56.442, 109.911, 296.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
FAD-binding protein


Mass: 46176.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomycetota bacterium (bacteria) / Gene: DIU60_24820
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
References: UniProt: A0A2W4MPG3
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Sugar
ChemComp-XUL / D-XYLULOSE


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Monosaccharides 0.1 M Buffer System 2 7.5 30 % v/v Precipitant Mix 1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.4→49.55 Å / Num. obs: 73369 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.071 / Rrim(I) all: 0.183 / Χ2: 1.04 / Net I/σ(I): 7.2
Reflection shellResolution: 2.4→2.45 Å / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 2.581 / Num. measured all: 30175 / Num. unique obs: 4513 / CC1/2: 0.587 / Rpim(I) all: 1.071 / Rrim(I) all: 2.798 / Χ2: 0.98 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→49.55 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 23.114 / SU ML: 0.426 / Cross valid method: THROUGHOUT / ESU R: 0.495 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28862 3654 5 %RANDOM
Rwork0.2463 ---
obs0.24838 69620 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.423 Å2
Baniso -1Baniso -2Baniso -3
1-10.06 Å20 Å20 Å2
2---2.28 Å20 Å2
3----7.78 Å2
Refinement stepCycle: 1 / Resolution: 2.4→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12414 0 252 44 12710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01313004
X-RAY DIFFRACTIONr_bond_other_d0.0020.01412074
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.64617779
X-RAY DIFFRACTIONr_angle_other_deg1.181.57627697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.97551615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.43819.743701
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.887151854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.42115133
X-RAY DIFFRACTIONr_chiral_restr0.0610.21659
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023029
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_it5.1897.0016496
X-RAY DIFFRACTIONr_mcbond_other5.1897.0016495
X-RAY DIFFRACTIONr_mcangle_it7.86910.4828099
X-RAY DIFFRACTIONr_mcangle_other7.86910.4838100
X-RAY DIFFRACTIONr_scbond_it4.7077.4346508
X-RAY DIFFRACTIONr_scbond_other4.7057.4346508
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.44610.9829681
X-RAY DIFFRACTIONr_long_range_B_refined10.70882.32814229
X-RAY DIFFRACTIONr_long_range_B_other10.70582.32414226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 265 -
Rwork0.454 5126 -
obs--99.8 %

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