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- PDB-9rvh: Tetrapodal ancestor of L-amino acid oxidase: Q225A-Loop (P361-PRE... -

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Basic information

Entry
Database: PDB / ID: 9rvh
TitleTetrapodal ancestor of L-amino acid oxidase: Q225A-Loop (P361-PREGA-L367) mutant with phenylalanine
ComponentsTetrapodal ancestor of L-amino acid oxidase: Q225A-Loop (P361-PREGA-L367) mutant with phenylalanine
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: 2.23 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: Q225A-Loop (P361-PREGA-L367) mutant with phenylalanine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5837
Polymers55,3091
Non-polymers1,2746
Water1,58588
1
A: Tetrapodal ancestor of L-amino acid oxidase: Q225A-Loop (P361-PREGA-L367) mutant with phenylalanine
hetero molecules

A: Tetrapodal ancestor of L-amino acid oxidase: Q225A-Loop (P361-PREGA-L367) mutant with phenylalanine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,16514
Polymers110,6172
Non-polymers2,54812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)94.405, 94.405, 189.443
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-630-

HOH

21A-668-

HOH

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Components

#1: Protein Tetrapodal ancestor of L-amino acid oxidase: Q225A-Loop (P361-PREGA-L367) mutant with phenylalanine


Mass: 55308.609 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 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 67.77 %
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: 2.23→94.4 Å / Num. obs: 41699 / % possible obs: 98.4 % / Redundancy: 6.9 % / CC1/2: 0.966 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.034 / Rrim(I) all: 0.091 / Χ2: 0.74 / Net I/σ(I): 10.2 / Num. measured all: 286718
Reflection shellResolution: 2.23→2.3 Å / % possible obs: 95.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 1.731 / Num. measured all: 24743 / Num. unique obs: 3694 / CC1/2: 0.439 / Rpim(I) all: 0.712 / Rrim(I) all: 1.876 / Χ2: 0.55 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→84.49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.886 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23652 2008 4.8 %RANDOM
Rwork0.20119 ---
obs0.20295 39632 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.23→84.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 85 88 4043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124047
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163806
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.8355472
X-RAY DIFFRACTIONr_angle_other_deg0.5871.7758763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.283531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66710687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02962
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_it5.0285.7661922
X-RAY DIFFRACTIONr_mcbond_other5.0275.7661922
X-RAY DIFFRACTIONr_mcangle_it7.10610.3622399
X-RAY DIFFRACTIONr_mcangle_other7.10510.3622400
X-RAY DIFFRACTIONr_scbond_it6.3576.3862125
X-RAY DIFFRACTIONr_scbond_other6.3566.3872126
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.22411.3983074
X-RAY DIFFRACTIONr_long_range_B_refined11.04155.434516
X-RAY DIFFRACTIONr_long_range_B_other11.04355.444511
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 124 -
Rwork0.347 2767 -
obs--94.29 %

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