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- PDB-3bjp: Urate oxidase cyanide uric acid ternary complex -

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Basic information

Entry
Database: PDB / ID: 3bjp
TitleUrate oxidase cyanide uric acid ternary complex
ComponentsUricase
KeywordsOXIDOREDUCTASE / uric acid / cyanide / inhibition / degradation mechanism / Acetylation / Peroxisome / Purine metabolism
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
ACETYL GROUP / CYANIDE ION / URIC ACID / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsGabison, L. / Prange, T. / Colloc'h, N. / El Hajji, M. / Castro, B. / Chiadmi, M.
CitationJournal: 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
DepositionDec 4, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4195
Polymers34,1581
Non-polymers2614
Water4,216234
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,67520
Polymers136,6304
Non-polymers1,04516
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 area26510 Å2
ΔGint-174 kcal/mol
Surface area43050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.936, 94.994, 104.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uricase / Urate oxidase


Mass: 34157.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase

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Non-polymers , 5 types, 238 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 8.5MG/ML URATE OXIDASE, 0.2M SODIUM CYANIDE, 50MM TRIS BUFFER, 0.5MG/ML URIC ACID, 10% PEG 8000, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 12, 2007 / Details: BENT MIRROR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 35679 / Num. obs: 32677 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 4.1 / % possible all: 98.4

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Processing

Software
NameClassification
SHELXLrefinement
SHELXL-97refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2ICQ

2icq


Resolution: 1.8→30 Å / Num. parameters: 10499 / Num. restraintsaints: 9869 / Isotropic thermal model: isotropic / Cross valid method: FREE R / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 2821 8 %RANDOM
Rwork0.2069 ---
all0.2139 35473 --
obs0.2106 32677 96.2 %-
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 2312 / Occupancy sum non hydrogen: 2612
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 18 234 2623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d0.075
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.322
X-RAY DIFFRACTIONs_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.032
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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