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- PDB-3obp: Anaerobic complex of urate oxidase with uric acid -

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Basic information

Entry
Database: PDB / ID: 3obp
TitleAnaerobic complex of urate oxidase with uric acid
ComponentsUricase
KeywordsOXIDOREDUCTASE / URIC ACID / INHIBITION / DEGRADATION MECHANISM / PEROXISOME / PURINE METABOLISM
Function / homology
Function and homology information


purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / 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: 1.5 Å
AuthorsGabison, L. / Chopard, C. / Colloc'h, N. / El Hajji, M. / Castro, B. / Chiadmi, M. / Prange, T.
CitationJournal: Proteins / Year: 2011
Title: X-ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor-less urate oxidase.
Authors: Gabison, L. / Chopard, C. / Colloc'h, N. / Peyrot, F. / Castro, B. / Hajji, M.E. / Altarsha, M. / Monard, G. / Chiadmi, M. / Prange, T.
History
DepositionAug 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_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

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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)34,3753
Polymers34,1841
Non-polymers1912
Water4,504250
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,49912
Polymers136,7344
Non-polymers7648
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 area25860 Å2
ΔGint-197 kcal/mol
Surface area44790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.853, 96.290, 105.737
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-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-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.: 250 / 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: 290 K / Method: liquide diffusion in gel phase / pH: 10.5
Details: SOLUTION A (0.1 ML): 50MM TRIS BUFFER, SATURATED WITH ACID URIC, 10% PEG 8000, PH 10.5, 0.5 MM AGAROSE IN CAPPILARY (HALF FILLING), SET AS A GEL (BY COOLING FROM 323 K TO ROOM TEMP). ...Details: SOLUTION A (0.1 ML): 50MM TRIS BUFFER, SATURATED WITH ACID URIC, 10% PEG 8000, PH 10.5, 0.5 MM AGAROSE IN CAPPILARY (HALF FILLING), SET AS A GEL (BY COOLING FROM 323 K TO ROOM TEMP). SOLUTION B (0.1 ML): 20 MG/ML PROTEIN, SAME BUFFER, SET IN CONTACT WITHIN THE CAPILLARY WITH SOL.A. CRYSTALS DEVELOP IN THE GEL PHASE BY SLOW DIFFUSION. ALL SOLUTION DEGASED, CRYSTALLIZATIONS UNDER ARGON ATMOSPHERE (ANAEROBIC CONDITIONS), liquide diffusion in gel phase, temperature 290K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2008 / Details: BENT MIRROR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→26.7 Å / Num. obs: 64921 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6068 / % possible all: 86.17

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Processing

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

2icq


Resolution: 1.5→10 Å / Num. parameters: 10619 / Num. restraintsaints: 9914 / Cross valid method: FREE R / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 3883 6 %RANDOM
Rwork0.2201 ---
all0.2302 64760 --
obs0.2277 60335 99.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 2314 / Occupancy sum non hydrogen: 2625
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 13 250 2625
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_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.049
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 1.5→1.55 Å
RfactorNum. reflection% reflection
Rfree0.297 370 -
Rwork0.283 --
obs-6068 6 %

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