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- PDB-4op9: Urate OXIDASE IN COMPLEX WITH 8-AZAXANTHINE -

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Basic information

Entry
Database: PDB / ID: 4op9
TitleUrate OXIDASE IN COMPLEX WITH 8-AZAXANTHINE
ComponentsUricase
KeywordsOXIDOREDUCTASE / HOMOTETRAMER / T-FOLD DOMAIN / PURISME METABOLISM / URIC ACID / PEROXISOME
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: 1.58 Å
AuthorsColloc'h, N. / Prange, T.
CitationJournal: Febs Lett. / Year: 2014
Title: Functional relevance of the internal hydrophobic cavity of urate oxidase.
Authors: Colloc'h, N. / Prange, T.
History
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references / Derived calculations
Category: reflns / struct_conn / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Sep 15, 2021Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _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_atom_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_atom_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 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
Water3,909217
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 area25890 Å2
ΔGint-158 kcal/mol
Surface area44290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.109, 96.175, 105.407
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 / Fragment: UNP residues 2-302
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-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3N5O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 291 K / Method: batch / pH: 8.5
Details: 10-15MG/ML URATE OXIDASE, 8-AZAXANTHIN IN EXCESS, 5-8% PEG8000, 50MM TRIS ACETATE, pH 8.5, BATCH, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.945 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 22, 2012 / Details: mirrors
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.945 Å / Relative weight: 1
ReflectionResolution: 1.58→70 Å / Num. obs: 55375 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 33.4
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2674 / % possible all: 95.6

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Processing

Software
NameClassification
MxCuBEdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: RIGID BODY
Starting model: 2IBA

2iba


Resolution: 1.58→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.293 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19055 2806 5.1 %RANDOM
Rwork0.16781 ---
obs0.16897 52567 98.69 %-
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: 22.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2---0.66 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 12 217 2591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9343324
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76524.701117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04515437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0231512
X-RAY DIFFRACTIONr_chiral_restr0.090.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211837
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.579→1.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 176 -
Rwork0.248 3577 -
obs--95.64 %

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