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- PDB-1xxj: Urate oxidase from aspergillus flavus complexed with 5-amino 6-ni... -

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Basic information

Entry
Database: PDB / ID: 1xxj
TitleUrate oxidase from aspergillus flavus complexed with 5-amino 6-nitro uracil
ComponentsUricase
KeywordsOXIDOREDUCTASE / uric acid degradation / dimeric barrel / tunnel-shaped protein
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / purine nucleobase catabolic process / 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
BENZENE / 5-AMINO-6-NITROPYRIMIDINE-2,4(1H,3H)-DIONE / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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.
History
DepositionNov 5, 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

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Assembly

Deposited unit
A: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,5659
Polymers136,7984
Non-polymers7675
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24680 Å2
ΔGint-100 kcal/mol
Surface area43080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.245, 142.265, 81.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Uricase / urate oxidase


Mass: 34199.586 Da / Num. of mol.: 4
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-UNC / 5-AMINO-6-NITROPYRIMIDINE-2,4(1H,3H)-DIONE / 5-AMINO 6-NITRO URACIL


Mass: 172.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4N4O4
#3: Chemical ChemComp-BNZ / BENZENE


Mass: 78.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8.5MG/ML PROTEIN, 0.2MG/ML DIAMINOURACIL, REM 5-7%(W/V) PEG 8000, 100MM TRIS/HCL, PH 8.0, NACACODYLATE 100mM pH 7.0, 1mM DTT, 1mM cymelarsan, pH 8.00, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.972 / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 2003 / Details: CURVATED MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.8→35 Å / Num. obs: 36394 / % possible obs: 98.7 % / Redundancy: 7 % / Rsym value: 0.069 / Net I/σ(I): 16.8
Reflection shellResolution: 2.8→2.88 Å / Mean I/σ(I) obs: 10.1 / Rsym value: 0.37 / % possible all: 98.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
BUSTER-TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRR

1wrr


Resolution: 2.8→15 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 3605 RANDOM
Rwork0.189 --
obs-36127 -
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9421 0 48 32 9501
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.108
X-RAY DIFFRACTIONt_dihedral_angle_d19.567
LS refinement shellResolution: 2.8→2.88 Å
RfactorNum. reflection
Rfree0.335 301
Rwork0.22 -
obs-3122

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