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- PDB-1xy3: Urate oxidase from aspergillus flavus complexed with guanine -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1xy3
TitleUrate oxidase from aspergillus flavus complexed with guanine
ComponentsUricase
KeywordsOXIDOREDUCTASE / uric acid degradation / dimeric barrel / tunnel-shaped protein
Function / homology
Function and homology information


purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome
Similarity search - Function
Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRetailleau, P. / Colloc'h, N. / Vivares, D. / Bonnete, F. / Castro, B. / El Hajji, M. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active site.
Authors: Retailleau, P. / Colloc'h, N. / Vivares, D. / Bonnete, F. / Castro, B. / El Hajji, M. / Prange, T.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the protein drug urate oxidase-inhibitor complex at 2.05 A resolution
Authors: Colloc'h, N. / El Hajji, M. / Bachet, B. / L'Hermite, G. / Schiltz, M. / Castro, B. / Mornon, J.P.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Complexed and ligand-free high-resolution structures of urate oxidase (Uox) from Aspergillus flavus: a reassignment of the active-site binding mode
Authors: Retailleau, P. / Colloc'h, N. / Vivares, D. / Bonnete, F. / Castro, B. / El Hajji, M. / Mornon, J.P. / Monard, G. / Prange, T.
History
DepositionNov 9, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,80616
Polymers273,5978
Non-polymers1,2098
Water00
1
A: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4038
Polymers136,7984
Non-polymers6054
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24640 Å2
ΔGint-102 kcal/mol
Surface area44720 Å2
MethodPISA
2
E: Uricase
F: Uricase
G: Uricase
H: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4038
Polymers136,7984
Non-polymers6054
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24700 Å2
ΔGint-101 kcal/mol
Surface area44340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.753, 141.936, 135.082
Angle α, β, γ (deg.)90.00, 92.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uricase / urate oxidase


Mass: 34199.586 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical
ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H5N5O

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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: 2.99 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8.5MG/ML PROTEIN, 0.2MG/ML GUANINE, 5-7%(W/V) PEG8000, 100MM TRIS/HCL, pH 8.00, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 48327 / % possible obs: 93.9 % / Redundancy: 3.1 % / Rsym value: 0.114 / Net I/σ(I): 9.4
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.6 / % possible all: 96

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
BUSTER-TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WWR

1wwr


Resolution: 3.2→15 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: GROUPED BFACTOR REFINEMENT
RfactorNum. reflectionSelection details
Rfree0.208 4804 RANDOM
Rwork0.172 --
obs-47923 -
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18857 0 88 0 18945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.007
X-RAY DIFFRACTIONx_angle_d0.691
X-RAY DIFFRACTIONt_dihedral_angle_d18.828

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