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- PDB-7p0g: URATE OXIDASE WITH 8-AZAXANTHINE UNDER AMBIENT PRESSURE -

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Basic information

Entry
Database: PDB / ID: 7p0g
TitleURATE OXIDASE WITH 8-AZAXANTHINE UNDER AMBIENT PRESSURE
ComponentsUricase
KeywordsOXIDOREDUCTASE / HPMX / purine metabolism / tetramer / T-fold domain / peroxisome
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / purine nucleobase catabolic process / urate catabolic process / peroxisome
Similarity search - Function
Uricase, conserved site / Uricase signature. / Uricase / Uricase
Similarity search - Domain/homology
8-AZAXANTHINE / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsColloc'h, N. / Prange, T. / Girard, E.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization.
Authors: Prange, T. / Carpentier, P. / Dhaussy, A.C. / van der Linden, P. / Girard, E. / Colloc'h, N.
History
DepositionJun 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Jul 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3603
Polymers34,1841
Non-polymers1762
Water4,702261
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,43912
Polymers136,7344
Non-polymers7048
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area26060 Å2
ΔGint-163 kcal/mol
Surface area44430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.341, 96.164, 105.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Uricase / Urate oxidase


Mass: 34183.590 Da / Num. of mol.: 1 / Fragment: URICASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.5
Details: 20 MG/ML URATE OXIDASE, 8-AZAXANTHINE CONCENTRATION IN EXCESS, 50 MM TRIS/ACETATE, 8% PEG 4000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: CRISTAL / Wavelength: 0.58183 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: Jul 28, 2019 / Details: mirrors
RadiationMonochromator: SI 111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.58183 Å / Relative weight: 1
ReflectionResolution: 1.9→26.765 Å / Num. obs: 30145 / % possible obs: 93.3 % / Redundancy: 3.6 % / Rsym value: 0.134 / Net I/σ(I): 6.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4400 / Rsym value: 0.514 / % possible all: 94.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.344
Highest resolutionLowest resolution
Rotation26.77 Å1.99 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0135refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1R51

1r51


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.1911 / WRfactor Rwork: 0.1516 / FOM work R set: 0.7983 / SU B: 3.748 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1511 / SU Rfree: 0.1469 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1390 5.1 %RANDOM
Rwork0.1743 ---
obs0.1768 25754 83.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 75.75 Å2 / Biso mean: 20.763 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å2-0 Å2
2---0.92 Å20 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 12 261 2635
Biso mean--12.59 34.28 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192480
X-RAY DIFFRACTIONr_bond_other_d0.0020.022315
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.9313364
X-RAY DIFFRACTIONr_angle_other_deg1.01235332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2315304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.05824.364118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77115430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.181513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022816
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02581
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 83 -
Rwork0.269 1746 -
all-1829 -
obs--77.47 %

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