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- PDB-4d13: Crystal structure of cofactor-free urate oxidase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4d13
TitleCrystal structure of cofactor-free urate oxidase in complex with its 5-peroxoisourate intermediate (X-ray dose, 2.2 kGy)
ComponentsURICASE
KeywordsOXIDOREDUCTASE / COFACTOR-FREE OXIDASE
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
5-(HYDRO)PEROXOISOURATE / Uricase
Similarity search - Component
Biological speciesASPERGILLUS FLAVUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.3 Å
AuthorsBui, S. / Steiner, R.A.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2014
Title: Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase.
Authors: Bui, S. / von Stetten, D. / Jambrina, P.G. / Prange, T. / Colloc'h, N. / de Sanctis, D. / Royant, A. / Rosta, E. / Steiner, R.A.
History
DepositionMay 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 13, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)34,6073
Polymers34,2891
Non-polymers3182
Water11,476637
1
A: URICASE
hetero molecules

A: URICASE
hetero molecules

A: URICASE
hetero molecules

A: URICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,42812
Polymers137,1554
Non-polymers1,2738
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area25470 Å2
ΔGint-130 kcal/mol
Surface area43540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.930, 95.080, 104.060
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-2145-

HOH

21A-2302-

HOH

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Components

#1: Protein URICASE / URATE OXIDASE


Mass: 34288.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FLAVUS (mold) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-IUP / 5-(HYDRO)PEROXOISOURATE


Mass: 200.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O5
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 57.4 % / Description: NONE
Crystal growpH: 8
Details: 20MG/ML UOX IN 50 MM TRIS-ACETATE PH 8.0 SATURATED WITH 9-METHYL URIC ACID UNDER ANAEROBIC CONDITIONS RESERVOIR: 8% PEG 8000, 50 MM TRIS-ACETATE PH 8.0 CRYSTALLIZATION WAS CARRIED OUT ...Details: 20MG/ML UOX IN 50 MM TRIS-ACETATE PH 8.0 SATURATED WITH 9-METHYL URIC ACID UNDER ANAEROBIC CONDITIONS RESERVOIR: 8% PEG 8000, 50 MM TRIS-ACETATE PH 8.0 CRYSTALLIZATION WAS CARRIED OUT ANAEROBICALLY. CRYSTALS WERE INCUBATED WITH A RESERVOIR SOLUTION ENRICHED BY 10 MM H2O2 AND 20% GLYCEROL TO GENERATE THE PEROXIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2013 / 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: 1.3→50 Å / Num. obs: 96758 / % possible obs: 99.6 % / Observed criterion σ(I): -1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.3→39.97 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.17 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.13155 4841 5 %RANDOM
Rwork0.10763 ---
obs0.10883 91916 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.027 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---0.35 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 22 637 3019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192723
X-RAY DIFFRACTIONr_bond_other_d0.0010.022578
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9453750
X-RAY DIFFRACTIONr_angle_other_deg0.7735985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023202
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02640
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0850.9761297
X-RAY DIFFRACTIONr_mcbond_other1.110.9791296
X-RAY DIFFRACTIONr_mcangle_it1.3771.4751647
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5991.1771426
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.82335301
X-RAY DIFFRACTIONr_sphericity_free37.915147
X-RAY DIFFRACTIONr_sphericity_bonded8.71655699
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 355 -
Rwork0.191 6671 -
obs--98.44 %

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