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- PDB-9qs1: Tetrapodal ancestor of L-amino acid oxidases -

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Basic information

Entry
Database: PDB / ID: 9qs1
TitleTetrapodal ancestor of L-amino acid oxidases
ComponentsTetrapodal ancestor of L-amino acis 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: 2.5 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 4, 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 acis oxidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3114
Polymers55,4411
Non-polymers8713
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-17 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.515, 94.515, 190.062
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-656-

HOH

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Components

#1: Protein Tetrapodal ancestor of L-amino acis 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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: NO3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: in 50 mM HEPES (pH 7.4), 500 mM NaCl, and 10% (v/v) glycerol

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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: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.5→190.06 Å / Num. obs: 30578 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.038 / Rrim(I) all: 0.135 / Χ2: 0.99 / Net I/σ(I): 14.2 / Num. measured all: 393838
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 99.4 % / Redundancy: 13.5 % / Rmerge(I) obs: 2.009 / Num. measured all: 45297 / Num. unique obs: 3364 / CC1/2: 0.636 / Rpim(I) all: 0.567 / Rrim(I) all: 2.089 / Χ2: 1 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→84.63 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.109 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24578 1582 5.2 %RANDOM
Rwork0.20491 ---
obs0.20701 28919 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 2.5→84.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 58 61 3997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124045
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163776
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6535481
X-RAY DIFFRACTIONr_angle_other_deg0.4951.5788695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.949531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42710691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02972
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_it4.6315.4421936
X-RAY DIFFRACTIONr_mcbond_other4.6315.4411936
X-RAY DIFFRACTIONr_mcangle_it6.5549.7852420
X-RAY DIFFRACTIONr_mcangle_other6.5549.7852421
X-RAY DIFFRACTIONr_scbond_it6.4596.082109
X-RAY DIFFRACTIONr_scbond_other6.4396.0772103
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.48910.8313059
X-RAY DIFFRACTIONr_long_range_B_refined12.00567.1817244
X-RAY DIFFRACTIONr_long_range_B_other12.00867.1217221
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 114 -
Rwork0.424 2082 -
obs--99.23 %

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