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- PDB-7puf: urate oxidase azaxanthine complex under 600 bar (60 MPa) of argon -

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Basic information

Entry
Database: PDB / ID: 7puf
Titleurate oxidase azaxanthine complex under 600 bar (60 MPa) of argon
ComponentsUricase
KeywordsOXIDOREDUCTASE / aspergillus flavus / homotetramer / argon / high pressure
Function / homology
Function and homology information


factor-independent urate hydroxylase / purine nucleobase catabolic process / urate oxidase activity / urate catabolic process / peroxisome
Similarity search - Function
Uricase, conserved site / Uricase signature. / Uricase / Uricase
Similarity search - Domain/homology
ARGON / 8-AZAXANTHINE / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsPrange, T. / Colloc'h, N. / Carpentier, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: 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.
#1: Journal: Current trends in X-ray crystallography / Year: 2011
Title: Current trends in X-ray Crystallography. Intech Open books
Authors: Colloc'h, N. / Marassio, G. / Prange, T.
#2: Journal: Journal of Applied Crystallography / Year: 2016
Title: Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel soak-and-freeze methodology
Authors: Lafumat, B. / Mueller-Dieckmann, C. / Leonard, G. / Colloc'h, N. / Prange, T. / Giraud, T. / Dobias, F. / Royant, A. / van der Linden, P. / Carpentier, P.
History
DepositionSep 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 13, 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
B: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,56110
Polymers67,0502
Non-polymers5128
Water9,746541
1
A: Uricase
B: Uricase
hetero molecules

A: Uricase
B: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,12320
Polymers134,0994
Non-polymers1,02416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area27090 Å2
ΔGint-159 kcal/mol
Surface area42940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.225, 95.268, 104.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uricase / Urate oxidase


Mass: 33524.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Komagataella pastoris (fungus)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-AR / ARGON


Mass: 39.948 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ar
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 8
Details: 20 microLiter (17 mg/mL protein, BUFFER Tris/Acetate pH 8) mixed with 20 microLiter PEG 4000 8% (same pH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2018
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 1.86→47.7 Å / Num. obs: 53842 / % possible obs: 81.5 % / Redundancy: 11.3 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 21.4
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 699 / CC1/2: 0.95 / Rpim(I) all: 0.151 / Rrim(I) all: 0.222 / % possible all: 20.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: dimer reconstructed from pdbid 1R51

1r51


Resolution: 1.86→47.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.558 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES :
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2726 5.1 %RANDOM
Rwork0.162 ---
obs0.164 51064 81.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90 Å2 / Biso mean: 17.38 Å2 / Biso min: 5.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.86→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4724 0 34 546 5304
Biso mean--19.81 27.49 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134993
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154655
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.6446780
X-RAY DIFFRACTIONr_angle_other_deg1.3031.58410762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9385620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18322.984258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12515887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.061525
X-RAY DIFFRACTIONr_chiral_restr0.0590.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021143
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

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