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- PDB-5m98: Crystal structure of urate oxidase from zebrafish -

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Basic information

Entry
Database: PDB / ID: 5m98
TitleCrystal structure of urate oxidase from zebrafish
ComponentsUricase
KeywordsOXIDOREDUCTASE / uric acid / urate / purine metabolism / uricolytic activities
Function / homology
Function and homology information


urate oxidase activity / purine nucleobase catabolic process / factor-independent urate hydroxylase / urate catabolic process / urate metabolic process / peroxisome / protein homotetramerization
Similarity search - Function
Urate Oxidase / Urate Oxidase; / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZanotti, G. / Cendron, l. / Percudani, R. / Berni, R.
CitationJournal: Sci Rep / Year: 2016
Title: Catalysis and Structure of Zebrafish Urate Oxidase Provide Insights into the Origin of Hyperuricemia in Hominoids.
Authors: Marchetti, M. / Liuzzi, A. / Fermi, B. / Corsini, R. / Folli, C. / Speranzini, V. / Gandolfi, F. / Bettati, S. / Ronda, L. / Cendron, L. / Berni, R. / Zanotti, G. / Percudani, R.
History
DepositionNov 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uricase
B: Uricase
C: Uricase
D: Uricase
E: Uricase
F: Uricase
G: Uricase
H: Uricase


Theoretical massNumber of molelcules
Total (without water)273,9148
Polymers273,9148
Non-polymers00
Water1,820101
1
A: Uricase
B: Uricase
C: Uricase
D: Uricase


Theoretical massNumber of molelcules
Total (without water)136,9574
Polymers136,9574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24800 Å2
ΔGint-153 kcal/mol
Surface area44740 Å2
MethodPISA
2
E: Uricase
F: Uricase
G: Uricase
H: Uricase


Theoretical massNumber of molelcules
Total (without water)136,9574
Polymers136,9574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24850 Å2
ΔGint-147 kcal/mol
Surface area44770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.341, 127.415, 132.604
Angle α, β, γ (deg.)90.00, 102.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uricase / Urate oxidase


Mass: 34239.238 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: uox / Production host: Escherichia coli (E. coli)
References: UniProt: Q6DG85, factor-independent urate hydroxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: Tris-HCl 0.1M, pH 8.5, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.8→83.3 Å / Num. obs: 64855 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 5.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.2 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→83.2 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.886 / SU B: 14.587 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.385
RfactorNum. reflection% reflectionSelection details
Rfree0.24168 3139 4.8 %RANDOM
Rwork0.20445 ---
obs0.20625 61716 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.04 Å2
2---0.04 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.8→83.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18584 0 0 101 18685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01919004
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.94525760
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63452288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91323.894904
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.464153376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.09215120
X-RAY DIFFRACTIONr_chiral_restr0.1050.22920
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114264
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.9812.9569176
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2674.42511456
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.393.119828
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.69139.26127317
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 203 -
Rwork0.309 4278 -
obs--88.89 %

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