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- PDB-4fsk: Urate oxidase-azide complex in anaerobic conditions -

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Basic information

Entry
Database: PDB / ID: 4fsk
TitleUrate oxidase-azide complex in anaerobic conditions
ComponentsUricase
KeywordsOXIDOREDUCTASE / INHIBITION / DEGRADATION MECHANISM / PEROXISOME / PURINE METABOLISM / HOMOTETRAMER / OXYGEN BINDING
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: 1.98 Å
AuthorsGabison, L. / Colloc'h, N. / El Hajji, M. / Castro, B. / Chiadmi, M. / Prange, T.
Citation
Journal: To be Published
Title: Azide and Cyanide Have Different Inhibition Modes of Urate Oxidase
Authors: Gabison, L. / Colloc'h, N. / El Hajji, M. / Castro, B. / Chiadmi, M. / 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. / El Hajji, M. / Castro, B. / Chiadmi, M.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 2.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 27, 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)34,3335
Polymers34,1841
Non-polymers1494
Water3,117173
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,33120
Polymers136,7344
Non-polymers59616
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 area26930 Å2
ΔGint-170 kcal/mol
Surface area42980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.858, 95.338, 104.777
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) / 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.: 3 / 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.: 173 / 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: 58.36 %
Crystal growTemperature: 291 K / pH: 10
Details: PROTEIN AT 20 MG/ML IN 50 MM TRIS BUFFER, 0.3 M SODIUM AZIDE, SATURATED WITH URIC ACID, pH 10.0, BATCH METHOD - STTING DROPS, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.982 / Wavelength: 0.982 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2009 / Details: BENT MIRROR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.982 Å / Relative weight: 1
ReflectionResolution: 1.98→38.23 Å / Num. all: 27917 / Num. obs: 26720 / % possible obs: 97.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 3.4
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 19.5 / % possible all: 93.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXLrefinement
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3P9F

3p9f


Resolution: 1.98→38.23 Å / Num. parameters: 10271 / Num. restraintsaints: 9872 / Cross valid method: NONE / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rwork0.189 ---
obs0.19 26720 98.7 %-
all-27917 --
Rfree---NONE
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2545.8
Refinement stepCycle: LAST / Resolution: 1.98→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 13 173 2545
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.034
X-RAY DIFFRACTIONs_angle_d0.077
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0258
X-RAY DIFFRACTIONs_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.027
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.073
X-RAY DIFFRACTIONs_approx_iso_adps

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