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- PDB-4oqc: Urate OXIDASE CO-CRYSTALLIZED WITH AZIDE -

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Basic information

Entry
Database: PDB / ID: 4oqc
TitleUrate OXIDASE CO-CRYSTALLIZED WITH AZIDE
ComponentsUricase
KeywordsOXYGEN BINDING / INHIBITION / DEGRADATION MECHANISM / PEROXISOME / PURINE METABOLISM / HETEROTETRAMER / COFACTORLESS OXIDASE
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
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsColloc'h, N. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Azide inhibition of urate oxidase.
Authors: Gabison, L. / Colloc'h, N. / Prange, T.
#1: Journal: Bmc Struct.Biol. / Year: 2008
Title: Structural Analysis of Urate Oxidase in Complex with its Natural Substrate Inhibited by Cyanide: Mechanistic Implications.
Authors: Gabison, L. / Prange, T. / Colloc'h, N. / Hajji, M.E. / Castro, B. / Chiadmi, M.
History
DepositionFeb 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Data collection
Revision 1.2Dec 28, 2016Group: Derived calculations
Revision 1.3Nov 8, 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_conn_type / 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 / _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.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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)34,2914
Polymers34,1841
Non-polymers1073
Water4,360242
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,16216
Polymers136,7344
Non-polymers42812
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 area26140 Å2
ΔGint-163 kcal/mol
Surface area42580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.770, 94.850, 104.340
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-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#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.: 242 / 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: 2.81 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 291 K / pH: 8.5
Details: PROTEIN AT 20 MG/ML IN 50 MM TRIS-ACETATE BUFFER, 0.3 M SODIUM AZIDE, PH 8.5 PRECIPITATING AGENT: PEG8000 18% IN TRIS BUFFER, BATCH METHOD, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.964
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2014 / 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: 1.3→15 Å / Num. obs: 89456 / % possible obs: 93.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.7
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.2 / % possible all: 94.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
SHELXL-97refinement
XDSdata reduction
SCALAdata scaling
TRUNCATEdata scaling
SHELXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3L8W

3l8w


Resolution: 1.3→10 Å / Num. parameters: 10515 / Num. restraintsaints: 9792 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflection
Rwork0.188 --
obs0.188 89456 93.3 %
all-89504 -
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 2260 / Occupancy sum non hydrogen: 2610.5
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 7 242 2611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d0.076
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0301
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.053
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps

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