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- PDB-7p0d: URATE OXIDASE WITH 8-AZAXANTHINE UNDER 310 MPA PRESSURE -

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Basic information

Entry
Database: PDB / ID: 7p0d
TitleURATE OXIDASE WITH 8-AZAXANTHINE UNDER 310 MPA 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: 2.4 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 1.2Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5134
Polymers34,1841
Non-polymers3293
Water2,072115
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,05116
Polymers136,7344
Non-polymers1,31712
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 area27430 Å2
ΔGint-143 kcal/mol
Surface area42930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.132, 95.398, 104.668
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.: 2 / 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.: 115 / 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: 2.89 Å3/Da / Density % sol: 57.43 %
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: 2.4→29.506 Å / Num. obs: 15109 / % possible obs: 96 % / Redundancy: 3.4 % / Rsym value: 0.139 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2216 / Rsym value: 0.635 / % possible all: 97.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.365
Highest resolutionLowest resolution
Rotation29.51 Å2.64 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 4OP9

4op9


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.426 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27 693 4.9 %RANDOM
Rwork0.188 ---
obs0.192 13313 88.4 %-
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: 114.89 Å2 / Biso mean: 49.02 Å2 / Biso min: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.85 Å20 Å20 Å2
2---0.46 Å20 Å2
3----2.39 Å2
Refinement stepCycle: final / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 23 115 2500
Biso mean--37.82 44.59 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192480
X-RAY DIFFRACTIONr_bond_other_d00.022305
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9353367
X-RAY DIFFRACTIONr_angle_other_deg3.80935311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8555302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59724.534118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.04415427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6451512
X-RAY DIFFRACTIONr_chiral_restr0.0720.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022814
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02580
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 50 -
Rwork0.349 869 -
all-919 -
obs--81.04 %

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