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- PDB-8ate: Galacturonic acid oxidase from Citrus sinensis -

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Basic information

Entry
Database: PDB / ID: 8ate
TitleGalacturonic acid oxidase from Citrus sinensis
ComponentsFAD-binding PCMH-type domain-containing protein
KeywordsFLAVOPROTEIN / Carbohydrate oxidation
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / IODIDE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesCitrus sinensis (sweet orange)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsBoverio, A. / Savino, S. / Fraaije, M.W. / Loncar, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemcatchem / Year: 2023
Title: Biochemical and Structural Characterization of a Uronic Acid Oxidase from Citrus sinensis
Authors: Boverio, A. / van Beek, H.L. / Savino, S. / Ranoux, A. / Huijgen, W.J.J. / Raaijmakers, H.W.C. / Fraaije, M.W. / Loncar, N.
History
DepositionAug 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: FAD-binding PCMH-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,86510
Polymers57,3241
Non-polymers1,5409
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.653, 101.653, 108.746
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein FAD-binding PCMH-type domain-containing protein


Mass: 57324.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: CISIN_1g015646mg / Cell line (production host): X-33 / Production host: Komagataella pastoris (fungus)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 92 molecules

#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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaI, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.92→108.75 Å / Num. obs: 45258 / % possible obs: 90 % / Redundancy: 15.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.022 / Rrim(I) all: 0.089 / Χ2: 1.03 / Net I/σ(I): 16.9 / Num. measured all: 714593
Reflection shellResolution: 1.92→1.96 Å / % possible obs: 99.4 % / Redundancy: 16.2 % / Rmerge(I) obs: 2.84 / Num. measured all: 53533 / Num. unique obs: 3312 / CC1/2: 0.63 / Rpim(I) all: 0.724 / Rrim(I) all: 2.932 / Χ2: 1.11 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.27data extraction
XDS0.7.2data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alpha fold

Resolution: 1.92→88.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.447 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24398 2309 5.1 %RANDOM
Rwork0.20532 ---
obs0.20719 42860 89.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.42 Å20 Å2
2--0.85 Å2-0 Å2
3----2.75 Å2
Refinement stepCycle: 1 / Resolution: 1.92→88.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 86 84 4156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134178
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173931
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.6495672
X-RAY DIFFRACTIONr_angle_other_deg1.3871.589032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3965501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09721.776214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13515682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5961527
X-RAY DIFFRACTIONr_chiral_restr0.0810.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021009
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_it4.0315.1612010
X-RAY DIFFRACTIONr_mcbond_other4.035.1612009
X-RAY DIFFRACTIONr_mcangle_it5.0577.7252509
X-RAY DIFFRACTIONr_mcangle_other5.0567.7262510
X-RAY DIFFRACTIONr_scbond_it4.6995.5012168
X-RAY DIFFRACTIONr_scbond_other4.7025.5012169
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5018.1093164
X-RAY DIFFRACTIONr_long_range_B_refined7.73560.3414811
X-RAY DIFFRACTIONr_long_range_B_other7.7460.3174803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.968 Å
RfactorNum. reflection% reflection
Rfree0.353 191 -
Rwork0.344 3445 -
obs--99.62 %

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