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- PDB-9qsn: Tetrapodal ancestor of L-amino acid oxidases co-crystallized with... -

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Basic information

Entry
Database: PDB / ID: 9qsn
TitleTetrapodal ancestor of L-amino acid oxidases co-crystallized with indole-3-acetic acid
ComponentsTetrapodal ancestor of L-amino acid oxidases
KeywordsOXIDOREDUCTASE / tryptophan / metabolic signaling / oxidation / FAD / snake venom / immunometabolism
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / NITRATE ION
Function and homology information
Biological speciesTetrapoda (tetrapods)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5346
Polymers55,4411
Non-polymers1,0945
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-9 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.312, 94.312, 190.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 3.82 Å3/Da / Density % sol: 67.79 %
Crystal growTemperature: 296 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-acetic acid

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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: Feb 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.34→47.2 Å / Num. obs: 37106 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.041 / Rrim(I) all: 0.147 / Χ2: 0.8 / Net I/σ(I): 11
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.712 / Num. unique obs: 3558 / CC1/2: 0.589 / Rpim(I) all: 0.518 / Rrim(I) all: 1.2 / Χ2: 0.52

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→47.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.206 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24151 1773 4.8 %RANDOM
Rwork0.20378 ---
obs0.20555 35259 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.189 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0 Å2
2--0.16 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.34→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 73 101 4052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124046
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163775
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.6535477
X-RAY DIFFRACTIONr_angle_other_deg0.4931.5788694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0755482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.229530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77410688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02965
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_it4.9515.7271931
X-RAY DIFFRACTIONr_mcbond_other4.9495.7271931
X-RAY DIFFRACTIONr_mcangle_it6.59310.2912412
X-RAY DIFFRACTIONr_mcangle_other6.59510.2912413
X-RAY DIFFRACTIONr_scbond_it6.3666.2982115
X-RAY DIFFRACTIONr_scbond_other6.376.2982113
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.11411.2613063
X-RAY DIFFRACTIONr_long_range_B_refined11.36269.7217312
X-RAY DIFFRACTIONr_long_range_B_other11.36469.6317292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.401 Å
RfactorNum. reflection% reflection
Rfree0.42 121 -
Rwork0.419 2503 -
obs--98.24 %

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