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- PDB-2fxl: Urate oxidase from aspergillus flavus complexed with allantoin -

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Basic information

Entry
Database: PDB / ID: 2fxl
TitleUrate oxidase from aspergillus flavus complexed with allantoin
ComponentsUricase
KeywordsOXIDOREDUCTASE / URIC ACID DEGRADATION / DIMERIC BARREL / TUNNEL-SHAPED PROTEIN / ALLANTOIN
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
1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.76 Å
AuthorsGabison, L. / Chiadmi, M. / Colloc'h, N. / Prange, T.
CitationJournal: Febs Lett. / Year: 2006
Title: Recapture of [S]-allantoin, the product of the two-step degradation of uric acid, by urate oxidase.
Authors: Gabison, L. / Chiadmi, M. / Colloc'h, N. / Castro, B. / El Hajji, M. / Prange, T.
History
DepositionFeb 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 28, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3562
Polymers34,2001
Non-polymers1561
Water3,027168
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4238
Polymers136,7984
Non-polymers6244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area24890 Å2
ΔGint-118 kcal/mol
Surface area43510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.364, 96.086, 105.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Uricase / Urate oxidase


Mass: 34199.586 Da / Num. of mol.: 1
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-2AL / 1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA / ALLANTOIN


Mass: 156.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: CRYSTALLIZATION CONDITIONS: 8.5MG/ML PROTEIN, EXCESS URIC ACID, 5-7% W/V PEG 8000, 100MM TRIS/HCL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.962 / Wavelength: 0.962 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 5, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.962 Å / Relative weight: 1
ReflectionResolution: 1.76→10.9 Å / Num. all: 39454 / Num. obs: 33267 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.064 / Net I/σ(I): 18.7
Reflection shellResolution: 1.76→1.85 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.287 / % possible all: 97.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXLrefinement
SHELXL-97refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1R4S

1r4s


Resolution: 1.76→10 Å / Num. parameters: 10259 / Num. restraintsaints: 9893 / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
all0.2073 39228 -
obs0.1906 33267 95.4 %
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 2318 / Occupancy sum non hydrogen: 2542
Refinement stepCycle: LAST / Resolution: 1.76→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 11 168 2541
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.036
X-RAY DIFFRACTIONs_angle_d0.079
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.028
X-RAY DIFFRACTIONs_from_restr_planes0.358
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.045

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