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- PDB-1wrr: Urate oxidase from aspergillus flavus complexed with 5-amino 6-ni... -

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Basic information

Entry
Database: PDB / ID: 1wrr
TitleUrate oxidase from aspergillus flavus complexed with 5-amino 6-nitro uracil
ComponentsUricase
KeywordsOXIDOREDUCTASE / uric acid degradation / dimeric barrel / tunnel-shaped protein
Function / homology
Function and homology information


purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / 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-AMINO-6-NITROPYRIMIDINE-2,4(1H,3H)-DIONE / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR under pressure of noble gaz / Resolution: 1.64 Å
AuthorsRetailleau, P. / Colloc'h, N. / Vivares, D. / Bonnete, F. / Castro, B. / El Hajji, M. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active site.
Authors: Retailleau, P. / Colloc'h, N. / Vivares, D. / Bonnete, F. / Castro, B. / El Hajji, M. / Prange, T.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the protein drug urate oxidase-inhibitor complex at 2.05 A resolution
Authors: Colloc'h, N. / El Hajji, M. / Bachet, B. / L'Hermite, G. / Schiltz, M. / Castro, B. / Mornon, J.P.
History
DepositionOct 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 28, 2018Group: Structure summary / Category: audit_author / Item: _audit_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)34,3722
Polymers34,2001
Non-polymers1721
Water3,873215
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4878
Polymers136,7984
Non-polymers6884
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 area24850 Å2
ΔGint-107 kcal/mol
Surface area44500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.385, 96.469, 106.131
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: 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-UNC / 5-AMINO-6-NITROPYRIMIDINE-2,4(1H,3H)-DIONE / 5-AMINO 6-NITRO URACIL


Mass: 172.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.8 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8.5MG/ML PROTEIN, 0.2MG/ML DIAMINOURACIL, 5-7%(W/V) PEG 8000, 100MM TRIS/HCL, pH 8.00, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 2003 / Details: curvated mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.64→35 Å / Num. obs: 48554 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 28.5 Å2 / Rsym value: 0.037 / Net I/σ(I): 17.8
Reflection shellResolution: 1.64→1.68 Å / Mean I/σ(I) obs: 10.3 / Rsym value: 0.285 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5refinement
SHARPphasing
RefinementMethod to determine structure: SIR under pressure of noble gaz
Resolution: 1.64→28 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.343 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: The structre was refined also with buster-TNT. The final refinement statistics were derived from REFMAC 5. Major refinement was proceeded using BUSTER-TNT.
RfactorNum. reflection% reflectionSelection details
Rfree0.18518 5098 10.1 %RANDOM
Rwork0.16798 ---
obs0.1697 45587 --
Solvent computationSolvent model: BABINET MASK
Displacement parametersBiso mean: 21.976 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---0.63 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.64→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 12 215 2589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222462
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9363341
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4455297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56224.655116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4315435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9611512
X-RAY DIFFRACTIONr_chiral_restr0.110.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021852
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2837
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21670
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.6271.51528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06222424
X-RAY DIFFRACTIONr_scbond_it4.58731076
X-RAY DIFFRACTIONr_scangle_it6.8344.5917
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 371 -
Rwork0.249 3301 -
obs--99.57 %

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