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- PDB-9rum: Tetrapodal ancestor of L-amino acid oxidase:Q225A single mutant -

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Basic information

Entry
Database: PDB / ID: 9rum
TitleTetrapodal ancestor of L-amino acid oxidase:Q225A single mutant
ComponentsTetrapodal ancestor of L-amino acid oxidase: Q225A 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: 2.79 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: Q225A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3049
Polymers54,8341
Non-polymers1,4708
Water1,13563
1
A: Tetrapodal ancestor of L-amino acid oxidase: Q225A mutant
hetero molecules

A: Tetrapodal ancestor of L-amino acid oxidase: Q225A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,60918
Polymers109,6682
Non-polymers2,94016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)94.801, 94.801, 189.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tetrapodal ancestor of L-amino acid oxidase: Q225A mutant


Mass: 54834.039 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 , 5 types, 71 molecules

#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.88 Å3/Da / Density % sol: 68.26 %
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: 2.79→189.17 Å / Num. obs: 21753 / % possible obs: 98.4 % / Redundancy: 5.6 % / CC1/2: 0.939 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.069 / Rrim(I) all: 0.169 / Χ2: 0.96 / Net I/σ(I): 6.7 / Num. measured all: 121492
Reflection shellResolution: 2.79→2.94 Å / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 1.239 / Num. measured all: 17540 / Num. unique obs: 3104 / CC1/2: 0.461 / Rpim(I) all: 0.552 / Rrim(I) all: 1.365 / Χ2: 0.96 / Net I/σ(I) obs: 1.1

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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: 2.79→84.75 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 17.924 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 0.601 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28445 1089 5 %RANDOM
Rwork0.21908 ---
obs0.22237 20536 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.844 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20 Å2
2--0.05 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.79→84.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 98 63 4035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124063
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163811
X-RAY DIFFRACTIONr_angle_refined_deg1.761.8315487
X-RAY DIFFRACTIONr_angle_other_deg0.6041.7728778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.495482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.747530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89410686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02963
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_it5.6366.3221931
X-RAY DIFFRACTIONr_mcbond_other5.6366.3221931
X-RAY DIFFRACTIONr_mcangle_it8.40911.3692412
X-RAY DIFFRACTIONr_mcangle_other8.40811.3692413
X-RAY DIFFRACTIONr_scbond_it6.3096.8362132
X-RAY DIFFRACTIONr_scbond_other6.3076.8372133
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.44512.2913076
X-RAY DIFFRACTIONr_long_range_B_refined11.913614540
X-RAY DIFFRACTIONr_long_range_B_other11.92660.154534
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.791→2.863 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 84 -
Rwork0.372 1470 -
obs--98.29 %

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