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- PDB-4d19: Crystal structure of cofactor-free urate oxidase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4d19
TitleCrystal structure of cofactor-free urate oxidase in complex with its 5-peroxoisourate intermediate (X-ray dose, 1.75 MGy)
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 / OXYGEN MOLECULE / URIC ACID / Uricase
Similarity search - Component
Biological speciesASPERGILLUS FLAVUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.35 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)34,8075
Polymers34,2891
Non-polymers5184
Water10,647591
1
A: URICASE
hetero molecules

A: URICASE
hetero molecules

A: URICASE
hetero molecules

A: URICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,22920
Polymers137,1554
Non-polymers2,07416
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 area27360 Å2
ΔGint-117.7 kcal/mol
Surface area43430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.940, 95.130, 104.110
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-2148-

HOH

21A-2297-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein URICASE / URATE OXIDASE / 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

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Non-polymers , 5 types, 595 molecules

#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: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#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.: 591 / 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.35→52.06 Å / Num. obs: 86674 / % possible obs: 99.7 % / Observed criterion σ(I): -1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.3
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.5 / % possible all: 99

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Processing

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

Resolution: 1.35→52.06 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.312 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.12973 4345 5 %RANDOM
Rwork0.10634 ---
obs0.10752 82329 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2---0.31 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.35→52.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 36 591 2987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192737
X-RAY DIFFRACTIONr_bond_other_d0.0010.022580
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9473769
X-RAY DIFFRACTIONr_angle_other_deg0.74735989
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_restr0.0820.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023272
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02642
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_it1.0911.0261299
X-RAY DIFFRACTIONr_mcbond_other1.0911.0261300
X-RAY DIFFRACTIONr_mcangle_it1.4181.5511648
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5181.2461438
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_restr1.52335317
X-RAY DIFFRACTIONr_sphericity_free39.5815141
X-RAY DIFFRACTIONr_sphericity_bonded9.55655715
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 337 -
Rwork0.19 5930 -
obs--98.9 %

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