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- PDB-4pr8: URATE OXIDASE AZIDE URIC ACID TERNARY complex -

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Basic information

Entry
Database: PDB / ID: 4pr8
TitleURATE OXIDASE AZIDE URIC ACID TERNARY complex
ComponentsUricase
KeywordsOXYGEN BINDING / INHIBITION / DEGRADATION MECHANISM / PEROXISOME / PURINE METABOLISM / HETEROTETRAMER / OXIDOREDUCTASE
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
AZIDE ION / URIC ACID / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.16 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
DepositionMar 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Derived calculations
Revision 1.2Nov 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_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.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 1.3Oct 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)34,4595
Polymers34,1841
Non-polymers2754
Water5,441302
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,83520
Polymers136,7344
Non-polymers1,10116
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 area27680 Å2
ΔGint-173 kcal/mol
Surface area42430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.577, 95.155, 104.823
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 2-296
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-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 302 / 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: batch method / pH: 8.5
Details: URATE OXIDASE COMPLEXED WITH 8-NITROXANTHINE (RED CRYSTALS-3LD4) SOAKED IN URIC ACID SOLUTION. AFTER LIGAND EXCHANGE, (COLORLESS CRYSTALS) THE CRYSTALS WERE INCUBATED WITH SODIUM AZIDE 0.3M, ...Details: URATE OXIDASE COMPLEXED WITH 8-NITROXANTHINE (RED CRYSTALS-3LD4) SOAKED IN URIC ACID SOLUTION. AFTER LIGAND EXCHANGE, (COLORLESS CRYSTALS) THE CRYSTALS WERE INCUBATED WITH SODIUM AZIDE 0.3M, 18% PEG8000, TRIS BUFFER PH=8.5 FOR 1/2 H., BATCH METHOD, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.938 / Wavelength: 0.938 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2014 / Details: BENT MIRROR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.938 Å / Relative weight: 1
ReflectionResolution: 1.158→47 Å / Num. all: 65154 / Num. obs: 65154 / % possible obs: 80.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.158-1.282.50.2722.112011134.2
1.28-102.50.05564.497842197.15

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Processing

Software
NameClassification
MxCuBEdata collection
SHELXmodel building
SHELXL-97refinement
XDSdata reduction
SCALAdata scaling
TRUNCATEdata scaling
SHELXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4FSK

4fsk


Resolution: 1.16→11 Å / Num. parameters: 18181 / Num. restraintsaints: 21705 / σ(F): 4
StereochEM target val spec case: NONE OTHER REFINEMENT REMARKS: MAIN CHAIN ATOMS (C, N, O, CA) ANISOTROPICALLY REFINED AS WELL AS WATER MOLECULES AND SODIUM ION. HYDROGENS KEPT AT THEORETICAL PLACES
Stereochemistry target values: ENGH AND HUBER
Details: MAIN CHAIN ATOMS (C, N, O, CA) ANISOTROPICALLY REFINED AS WELL AS WATER MOLECULES AND SODIUM ION. HYDROGENS KEPT AT THEORETICAL PLACES
RfactorNum. reflection% reflection
Rwork0.184 --
obs0.184 65154 80.9 %
all-65154 -
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 2294 / Occupancy sum non hydrogen: 2684.4
Refinement stepCycle: LAST / Resolution: 1.16→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 19 302 2683
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0256
X-RAY DIFFRACTIONs_angle_d0.0703
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.4012
X-RAY DIFFRACTIONs_zero_chiral_vol0.0465
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.0574
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0263
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0413
X-RAY DIFFRACTIONs_approx_iso_adps0.0603

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