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- PDB-4cw2: Crystal structure of cofactor-free urate oxidase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4cw2
TitleCrystal structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-metyl uric acid (X-ray dose, 2.5 kGy)
ComponentsURICASEUrate oxidase
KeywordsOXIDOREDUCTASE / COFACTOR-FREE OXIDASE
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / purine nucleobase metabolic 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 / OTHER / Resolution: 1.32 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

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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)34,5323
Polymers34,2001
Non-polymers3322
Water11,259625
1
A: URICASE
hetero molecules

A: URICASE
hetero molecules

A: URICASE
hetero molecules

A: URICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,12812
Polymers136,7984
Non-polymers1,3298
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 area23940 Å2
ΔGint-129.3 kcal/mol
Surface area47410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.506, 95.132, 104.310
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 / 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
#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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 625 / 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 EXPOSED TO AIR TO GENERATE THE PEROXIDE

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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: 1.32→50 Å / Num. obs: 92669 / % possible obs: 100 % / Observed criterion σ(I): -1 / Redundancy: 6.6 % / Biso Wilson estimate: 10.82 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.8
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / % 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: 1.32→70.29 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.418 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.035 / 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
Rfree0.13696 4635 5 %RANDOM
Rwork0.11044 ---
obs0.11178 88023 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: 15.409 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2--0.71 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.32→70.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 23 625 3057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192732
X-RAY DIFFRACTIONr_bond_other_d0.0020.022605
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9513754
X-RAY DIFFRACTIONr_angle_other_deg0.85536045
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_restr0.0980.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023174
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_it2.6821.1441294
X-RAY DIFFRACTIONr_mcbond_other2.6811.1441295
X-RAY DIFFRACTIONr_mcangle_it3.0371.7181635
X-RAY DIFFRACTIONr_mcangle_other3.0371.7191635
X-RAY DIFFRACTIONr_scbond_it2.6611.3721438
X-RAY DIFFRACTIONr_scbond_other2.661.3721439
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5031.9562093
X-RAY DIFFRACTIONr_long_range_B_refined7.76615.8272807
X-RAY DIFFRACTIONr_long_range_B_other5.43913.172342
X-RAY DIFFRACTIONr_rigid_bond_restr3.13135337
X-RAY DIFFRACTIONr_sphericity_free60.785168
X-RAY DIFFRACTIONr_sphericity_bonded16.31755732
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 335 -
Rwork0.237 6449 -
obs--99.91 %

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