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- PDB-9rvj: Tetrapodal ancestor of L-amino acid oxidases: W377I double mutant... -

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Basic information

Entry
Database: PDB / ID: 9rvj
TitleTetrapodal ancestor of L-amino acid oxidases: W377I double mutant with phenylalanine
ComponentsTetrapodal ancestor of L-amino acid oxidase: Q225H - W377I double mutant with phenylalanine
KeywordsOXIDOREDUCTASE / tryptophan / metabolic signaling / oxidation / FAD / snake venom / immunometabolism
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / PHENYLACETALDEHYDE / DI(HYDROXYETHYL)ETHER / PHENYLALANINE
Function and homology information
Biological speciesTetrapoda (tetrapods)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Tetrapodal ancestor of L-amino acid oxidase: Q225H - W377I double mutant with phenylalanine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,55811
Polymers54,8281
Non-polymers1,73010
Water2,684149
1
A: Tetrapodal ancestor of L-amino acid oxidase: Q225H - W377I double mutant with phenylalanine
hetero molecules

A: Tetrapodal ancestor of L-amino acid oxidase: Q225H - W377I double mutant with phenylalanine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,11522
Polymers109,6562
Non-polymers3,45920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)94.234, 94.234, 191.730
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-660-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 54828.051 Da / Num. of mol.: 1
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 , 6 types, 159 molecules

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


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-HY1 / PHENYLACETALDEHYDE


Mass: 120.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O
#6: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.87 Å3/Da / Density % sol: 68.23 %
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: Apr 22, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.3→46.12 Å / Num. obs: 38980 / % possible obs: 99.5 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.044 / Rrim(I) all: 0.125 / Χ2: 1.08 / Net I/σ(I): 14 / Num. measured all: 293617
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 99.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 1.081 / Num. measured all: 29517 / Num. unique obs: 3752 / CC1/2: 0.579 / Rpim(I) all: 0.401 / Rrim(I) all: 1.158 / Χ2: 1.11 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.12 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.628 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21707 1875 4.8 %RANDOM
Rwork0.17691 ---
obs0.17882 37028 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.3→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 105 149 4139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124080
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163826
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.8325510
X-RAY DIFFRACTIONr_angle_other_deg0.6211.7738811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.793530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06910689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02970
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_it3.3533.8781936
X-RAY DIFFRACTIONr_mcbond_other3.3523.8781937
X-RAY DIFFRACTIONr_mcangle_it4.8496.9552415
X-RAY DIFFRACTIONr_mcangle_other4.8486.9552416
X-RAY DIFFRACTIONr_scbond_it5.0184.4412144
X-RAY DIFFRACTIONr_scbond_other5.0174.4412145
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4937.8553096
X-RAY DIFFRACTIONr_long_range_B_refined8.78538.314559
X-RAY DIFFRACTIONr_long_range_B_other8.78538.314560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 126 -
Rwork0.273 2687 -
obs--99.75 %

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