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- PDB-3cku: Urate oxidase from aspergillus flavus complexed with its inhibito... -

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Basic information

Entry
Database: PDB / ID: 3cku
TitleUrate oxidase from aspergillus flavus complexed with its inhibitor 8-azaxanthin and chloride
ComponentsUricase
KeywordsOXIDOREDUCTASE / URIC ACID DEGRADATION / 8-AZAXHANTIN
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
8-AZAXANTHINE / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsColloc'h, N. / Prange, T.
Citation
Journal: Biophys.J. / Year: 2008
Title: Oxygen pressurized X-ray crystallography: probing the dioxygen binding site in cofactorless urate oxidase and implications for its catalytic mechanism.
Authors: Colloc'h, N. / Gabison, L. / Monard, G. / Altarsha, M. / Chiadmi, M. / Marassio, G. / Sopkova-de Oliveira Santos, J. / El Hajji, M. / Castro, B. / Abraini, J.H. / 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.
#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.
#3: Journal: Biophys.J. / Year: 2007
Title: Protein crystallography under xenon and nitrous oxide pressure: comparison with in vivo pharmacology studies and implications for the mechanism of inhaled anesthetic action.
Authors: Colloc'h, N. / Sopkova-de Oliveira Santos, J. / Retailleau, P. / Vivares, D. / Bonnete, F. / Langlois d'Estainto, B. / Gallois, B. / Brisson, A. / Risso, J.J. / Lemaire, M. / Prange, T. / Abraini, J.H.
History
DepositionMar 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3954
Polymers34,1841
Non-polymers2123
Water4,954275
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,58116
Polymers136,7344
Non-polymers84612
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 area26430 Å2
ΔGint-212.6 kcal/mol
Surface area42840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.994, 94.979, 104.381
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: 34183.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Genus: UAZ, UOX / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3N5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2MG/ML 8-AZAXANTHIN, 0.3M SODIUM CHLORIDE, 0.05M TRIS/HCL, 10-15% W/V PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.964 / Wavelength: 0.964 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2007 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. all: 43251 / Num. obs: 42048 / % possible obs: 99.63 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.0555 / Rsym value: 0.0531 / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 13.7 / Num. unique all: 6302 / Rsym value: 0.084 / % possible all: 100

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1R4S

1r4s


Resolution: 1.7→10 Å / Num. parameters: 10759 / Num. restraintsaints: 9913 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3340 8 %RANDOM
Rwork0.193 ---
all0.2 43014 --
obs0.197 42048 99.4 %-
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2651
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 16 275 2687
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.033
X-RAY DIFFRACTIONs_angle_d0.077
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0285
X-RAY DIFFRACTIONs_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0

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