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- PDB-9qso: Tetrapodal ancestor of L-amino acid oxidases co-crystallised with... -

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Basic information

Entry
Database: PDB / ID: 9qso
TitleTetrapodal ancestor of L-amino acid oxidases co-crystallised with indole-3-pyruvate
ComponentsTetrapodal ancestor of L-amino acid oxidases co-crystallised
KeywordsOXIDOREDUCTASE / tryptophan / metabolic signaling / oxidation / FAD / snake venom / immunometabolism
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesTetrapoda (tetrapods)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsMassari, M. / Mattevi, A.
Funding support Italy, 2items
OrganizationGrant numberCountry
Italian Association for Cancer Research26648 Italy
Italian Ministry of EducationP2022FESRR Italy
CitationJournal: To Be Published
Title: Evolution of Human IL4i1 Preference for Aromatic Amino Acids from a Broad-Specificity L-Amino Acid Oxidase Ancestor
Authors: Massari, M. / Mattevi, A.
History
DepositionApr 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetrapodal ancestor of L-amino acid oxidases co-crystallised
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5165
Polymers55,4411
Non-polymers1,0764
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-8 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.532, 95.532, 187.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

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Components

#1: Protein Tetrapodal ancestor of L-amino acid oxidases co-crystallised


Mass: 55440.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrapoda (tetrapods) / Production host: Escherichia coli BL21 (bacteria)
#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.: 32 / Source method: isolated from a natural source / Formula: H2O
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: 3.86 Å3/Da / Density % sol: 68.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM HEPES (pH 7.4), 500 mM NaCl, and 10% (v/v) glycerol, 10 mM indole-3-pyruvate

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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 6M / Detector: PIXEL / Date: Nov 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.98→47.81 Å / Num. obs: 18521 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.063 / Rrim(I) all: 0.227 / Χ2: 1.01 / Net I/σ(I): 10.7
Reflection shellResolution: 2.98→3.08 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.8 / Num. unique obs: 1785 / CC1/2: 0.488 / Rpim(I) all: 0.892 / Rrim(I) all: 1.2 / Χ2: 0.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→47.81 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.873 / SU B: 38.96 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 1.108 / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28909 948 5.1 %RANDOM
Rwork0.22017 ---
obs0.22361 17510 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å20 Å2
2---0.42 Å20 Å2
3---0.84 Å2
Refinement stepCycle: 1 / Resolution: 2.98→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 72 32 3982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124077
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163811
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.6535517
X-RAY DIFFRACTIONr_angle_other_deg0.481.5798778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02973
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_it5.0996.0931936
X-RAY DIFFRACTIONr_mcbond_other5.0966.0921936
X-RAY DIFFRACTIONr_mcangle_it7.69710.9442420
X-RAY DIFFRACTIONr_mcangle_other7.69710.9432421
X-RAY DIFFRACTIONr_scbond_it6.6356.6912141
X-RAY DIFFRACTIONr_scbond_other6.6346.6912142
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.91312.0453098
X-RAY DIFFRACTIONr_long_range_B_refined13.82475.1717941
X-RAY DIFFRACTIONr_long_range_B_other13.82475.1717941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.98→3.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.549 59 -
Rwork0.549 1264 -
obs--99.7 %

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