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- PDB-4cw6: Crystal structure of cofactor-free urate oxidase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4cw6
TitleCrystal structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-metyl uric acid (X-ray dose, 92 kGy)
ComponentsURICASE
KeywordsOXIDOREDUCTASE / COFACTOR-FREE OXIDASE
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
9-METHYL URIC ACID / OXYGEN MOLECULE / Chem-XDS / Uricase
Similarity search - Component
Biological speciesASPERGILLUS FLAVUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.28 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
DepositionApr 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jun 21, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 20, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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 1.5Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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

Downloads & links

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Assembly

Deposited unit
A: URICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7465
Polymers34,2001
Non-polymers5464
Water10,665592
1
A: URICASE
hetero molecules

A: URICASE
hetero molecules

A: URICASE
hetero molecules

A: URICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,98420
Polymers136,7984
Non-polymers2,18616
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 area24430 Å2
ΔGint-123.6 kcal/mol
Surface area47450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.501, 95.138, 104.354
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-2304-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein URICASE / URATE OXIDASE


Mass: 34199.586 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, 596 molecules

#2: Chemical ChemComp-XDS / (5S)-5-(dioxidanyl)-9-methyl-7H-purine-2,6,8-trione


Mass: 214.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4O5
#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-MUA / 9-METHYL URIC ACID


Mass: 182.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.8 Å3/Da / Density % sol: 57.4 % / Description: NONE
Crystal growpH: 8 / Details: LIKE PDB CODE 4CW2, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 101601 / % possible obs: 99.9 % / Observed criterion σ(I): -1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 1.28→1.32 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

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

Resolution: 1.28→40 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.227 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.13212 5076 5 %RANDOM
Rwork0.11212 ---
obs0.1131 96521 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.746 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2--0.73 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.28→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 38 592 3039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192741
X-RAY DIFFRACTIONr_bond_other_d0.0030.022606
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9543765
X-RAY DIFFRACTIONr_angle_other_deg0.85536044
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_restr0.1030.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02631
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_it2.721.1651293
X-RAY DIFFRACTIONr_mcbond_other2.721.1651293
X-RAY DIFFRACTIONr_mcangle_it3.0941.7491633
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4561.3871448
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_restr3.07435347
X-RAY DIFFRACTIONr_sphericity_free62.2755160
X-RAY DIFFRACTIONr_sphericity_bonded19.4755743
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 400 -
Rwork0.261 7059 -
obs--99.85 %

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