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- PDB-3p9o: Aerobic ternary complex of urate oxidase with azide and chloride -

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Basic information

Entry
Database: PDB / ID: 3p9o
TitleAerobic ternary complex of urate oxidase with azide and chloride
ComponentsUricaseUrate oxidase
KeywordsOXYGEN BINDING / URIC ACID / INHIBITION / DEGRADATION MECHANISM / PEROXISOME / PURINE METABOLISM / AZIDE / OXYGEN BINDING OXIDOREDUCTASE
Function / homology
Function and homology information


purine nucleobase catabolic process / urate oxidase activity / 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
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsGabison, L. / Colloc'H, N. / El Hajji, M. / Castro, B. / Chiadmi, M. / Prange, T.
Citation
Journal: To be Published
Title: Azide and Cyanide Show Different Inhibition Modes to 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
DepositionOct 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4107
Polymers34,1841
Non-polymers2276
Water6,900383
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,64028
Polymers136,7344
Non-polymers90624
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 area28020 Å2
ΔGint-203 kcal/mol
Surface area42770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.493, 94.993, 104.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1382-

HOH

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Components

#1: Protein Uricase / Urate oxidase / 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 / Azide


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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 / Water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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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: 57.26 %
Crystal growTemperature: 291 K / pH: 10
Details: SOLUTION A (0.1 ML): 50MM TRIS BUFFER, 0.3 M SODIUM AZIDE, SATURATED WITH URIC ACID BUFFER, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 10.0

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.982
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: 1.45→39.7 Å / Num. obs: 69903 / % possible obs: 99.4 % / Observed criterion σ(I): 4 / Redundancy: 5.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.5
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 3.8 / % possible all: 97.1

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Processing

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

3l8w


Resolution: 1.45→39.7 Å / Num. parameters: 11299 / Num. restraintsaints: 10091 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.255 4202 6 %RANDOM
Rwork0.201 ---
all-69656 --
obs-69656 99.4 %-
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2754.95
Refinement stepCycle: LAST / Resolution: 1.45→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 14 383 2759
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.032
X-RAY DIFFRACTIONs_angle_d0.078
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.057
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps

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