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- PDB-2iba: Urate oxidase from Aspergillus flavus complexed with its inhibito... -

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Basic information

Entry
Database: PDB / ID: 2iba
TitleUrate oxidase from Aspergillus flavus complexed with its inhibitor 8-azaxanthine
ComponentsUricase
KeywordsOXIDOREDUCTASE / uric acid degradation / T-fold domain / tetrameric enzyme
Function / homology
Function and homology information


urate oxidase activity / purine nucleobase catabolic process / factor-independent urate hydroxylase / 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 / RIGID BODY / Resolution: 1.5 Å
AuthorsColloc'h, N. / Retailleau, P. / Sopkova-de Oliveira Santos, J. / Prange, T.
Citation
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. / Langlois d'Estainto, B. / Gallois, B. / Brisson, A. / Risso, J.J. / Lemaire, M. / Abraini, J.H.
#1: 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
DepositionSep 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_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 1.5Oct 30, 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)34,3603
Polymers34,1841
Non-polymers1762
Water3,765209
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,43912
Polymers136,7344
Non-polymers7048
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 area25960 Å2
ΔGint-158 kcal/mol
Surface area43930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.492, 96.041, 105.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Detailsfunctionnal homotetramer

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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) / Gene: uaZ, uox / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 10MG/ML URATE OXIDASE, 8-AZAXANTHINE 0.2MG/ML, TRIS 20mM, PEG 8000 7%, NACL 200mM, batch, TEMPERATURE 298K, PH 8.5

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2005
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 65481 / Num. obs: 59653 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 18.06 Å2 / Rmerge(I) obs: 0.056 / Χ2: 0.726 / Net I/σ(I): 10.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.271 / Num. unique all: 5710 / Χ2: 0.367 / % possible all: 87.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
RefinementMethod to determine structure: RIGID BODY
Starting model: PDB ENTRY 1R51

1r51


Resolution: 1.5→14.87 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.147 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3021 5.1 %RANDOM
Rwork0.176 ---
obs0.177 59516 90.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.872 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→14.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 12 209 2583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222454
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9343327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72224.746118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49115437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6611512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021841
X-RAY DIFFRACTIONr_nbd_refined0.2010.2930
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21680
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2153
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.230
X-RAY DIFFRACTIONr_mcbond_it0.7881.51471
X-RAY DIFFRACTIONr_mcangle_it1.522403
X-RAY DIFFRACTIONr_scbond_it2.16531032
X-RAY DIFFRACTIONr_scangle_it3.5644.5924
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 204 -
Rwork0.261 3878 -
obs-4082 85.72 %

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