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- PDB-9run: Tetrapodal ancestor of L-amino acid oxidase: W377I mutant -

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Basic information

Entry
Database: PDB / ID: 9run
TitleTetrapodal ancestor of L-amino acid oxidase: W377I mutant
ComponentsTetrapodal ancestor of L-amino acid oxidase: Q225H-W377I double mutant
KeywordsOXIDOREDUCTASE / tryptophan / metabolic signaling / oxidation / FAD / snake venom / immunometabolism
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / NITRATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesTetrapoda (tetrapods)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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
DepositionJul 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 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 oxidase: Q225H-W377I double mutant
B: Tetrapodal ancestor of L-amino acid oxidase: Q225H-W377I double mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,08913
Polymers110,7352
Non-polymers2,35411
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-15 kcal/mol
Surface area35710 Å2
Unit cell
Length a, b, c (Å)90.340, 95.664, 173.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tetrapodal ancestor of L-amino acid oxidase: Q225H-W377I double mutant


Mass: 55367.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrapoda (tetrapods) / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 5 types, 187 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / 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.: 6 / 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.2 M sodium nitrate, 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 6M / Detector: PIXEL / Date: Jun 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.26→95.66 Å / Num. obs: 69791 / % possible obs: 98 % / Redundancy: 4.5 % / CC1/2: 0.986 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.084 / Rrim(I) all: 0.19 / Χ2: 0.95 / Net I/σ(I): 4.9 / Num. measured all: 314348
Reflection shellResolution: 2.26→2.31 Å / % possible obs: 92.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 1.413 / Num. measured all: 18132 / Num. unique obs: 4203 / CC1/2: 0.392 / Rpim(I) all: 0.726 / Rrim(I) all: 1.598 / Χ2: 0.98 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→80.15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.211 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25271 3589 5.2 %RANDOM
Rwork0.20482 ---
obs0.2073 65849 97 %-
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
1-0.03 Å2-0 Å20 Å2
2---0 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.26→80.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7744 0 157 176 8077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0128083
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167563
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.83210936
X-RAY DIFFRACTIONr_angle_other_deg0.6361.77417421
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_restr0.0890.21181
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021918
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_it3.9954.2213862
X-RAY DIFFRACTIONr_mcbond_other3.9914.2213862
X-RAY DIFFRACTIONr_mcangle_it5.5137.584824
X-RAY DIFFRACTIONr_mcangle_other5.5127.5814825
X-RAY DIFFRACTIONr_scbond_it5.4344.7884221
X-RAY DIFFRACTIONr_scbond_other5.4344.7884222
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0358.4996113
X-RAY DIFFRACTIONr_long_range_B_refined9.55840.318890
X-RAY DIFFRACTIONr_long_range_B_other9.56140.318875
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.315 Å
RfactorNum. reflection% reflection
Rfree0.345 231 -
Rwork0.343 4602 -
obs--92.3 %

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