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- PDB-1r56: UNCOMPLEXED URATE OXIDASE FROM ASPERGILLUS FLAVUS -

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Basic information

Entry
Database: PDB / ID: 1r56
TitleUNCOMPLEXED URATE OXIDASE FROM ASPERGILLUS FLAVUS
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
DI(HYDROXYETHYL)ETHER / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRetailleau, P. / Colloc'h, N. / Prange, T.
Citation
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.
#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. / Prange, T. / Castro, B. / Mornon, J.P.
History
DepositionOct 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 1.4Aug 23, 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)273,80910
Polymers273,5978
Non-polymers2122
Water6,017334
1
A: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,0116
Polymers136,7984
Non-polymers2122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23570 Å2
ΔGint-110 kcal/mol
Surface area45280 Å2
MethodPISA
2
E: Uricase
F: Uricase
G: Uricase
H: Uricase


Theoretical massNumber of molelcules
Total (without water)136,7984
Polymers136,7984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22970 Å2
ΔGint-118 kcal/mol
Surface area44880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.590, 141.843, 134.959
Angle α, β, γ (deg.)90.00, 92.69, 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 natural source / Source: (natural) Aspergillus flavus (mold)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.89 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 291 K / pH: 8
Details: 8.5MG/ML PROTEIN, 5-7% W/V PEG 8000, 100MM TRIS/HCL, temperature 291K, pH 8.00

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→32 Å / Num. obs: 136450 / % possible obs: 99.2 % / Redundancy: 5.2 % / Rsym value: 0.076 / Net I/σ(I): 12.3
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.6 / % possible all: 98.3

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Processing

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

1uox
PDB Unreleased entry


Resolution: 2.3→10 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.214 13478
Rwork0.162 -
obs-134760
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18898 0 0 342 19240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.275
X-RAY DIFFRACTIONt_dihedral_angle_d18.65
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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