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- PDB-2zkb: Urate oxidase complexed with 8-azaxanthine under 2.5 MPa oxygen p... -

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Basic information

Entry
Database: PDB / ID: 2zkb
TitleUrate oxidase complexed with 8-azaxanthine under 2.5 MPa oxygen pressure
ComponentsUricase
KeywordsOXIDOREDUCTASE / URIC ACID DEGRADATION / GAZ-PROTEIN COMPLEX / T-FOLD DOMAIN / ACETYLATION / PEROXISOME / PURINE METABOLISM / tetramer
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
8-AZAXANTHINE / OXYGEN MOLECULE / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body / Resolution: 1.61 Å
AuthorsColloc'h, N. / Gabison, L. / Chiadmi, M. / Abraini, J.H. / Prange, T.
CitationJournal: Biophys.J. / Year: 2008
Title: Oxygen pressurized X-ray crystallography: probing the dioxygen binding site in cofactorless urate oxidase and implications for its catalytic mechanism.
Authors: Colloc'h, N. / Gabison, L. / Monard, G. / Altarsha, M. / Chiadmi, M. / Marassio, G. / Sopkova-de Oliveira Santos, J. / El Hajji, M. / Castro, B. / Abraini, J.H. / Prange, T.
History
DepositionMar 14, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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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)34,3924
Polymers34,1841
Non-polymers2083
Water3,459192
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,56716
Polymers136,7344
Non-polymers83212
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 area26430 Å2
ΔGint-157.2 kcal/mol
Surface area44100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.753, 96.285, 105.427
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3N5O2
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10 mg/ml urate oxidase, 0.2mg/ml 8-azaxanthine, 50mM Tris, 20mM NaCl, PEG 8000 4-10%, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2005 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. all: 52825 / Num. obs: 52204 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.9
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 3 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.15 / Num. unique all: 5133 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: rigid body
Starting model: 2IBA
Resolution: 1.61→14.96 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.457 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19509 2658 5.1 %RANDOM
Rwork0.17519 ---
obs0.17622 49475 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.718 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.61→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 17 192 2588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9343318
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7524.655116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15415434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.61512
X-RAY DIFFRACTIONr_chiral_restr0.1020.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021833
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2892
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21670
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.2102
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.871.51471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6422401
X-RAY DIFFRACTIONr_scbond_it2.46131026
X-RAY DIFFRACTIONr_scangle_it4.0564.5917
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.609→1.651 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 196 -
Rwork0.261 3478 -
obs--96 %

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