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- PDB-1vay: Crystal Structure of Uricase from Arthrobacter globiformis with i... -

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Basic information

Entry
Database: PDB / ID: 1vay
TitleCrystal Structure of Uricase from Arthrobacter globiformis with inhibitor 8-azaxanthine
ComponentsUric acid oxidase
KeywordsOXIDOREDUCTASE
Function / homologyUrate Oxidase / Urate Oxidase; / Roll / Alpha Beta / 8-AZAXANTHINE
Function and homology information
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsHossain, M.T. / Suzuki, K. / Yamamoto, T. / Imamura, S. / Sekiguchi, T. / Takenaka, A.
CitationJournal: To be Published
Title: Crystal Structure of Uricase from Arthrobacter Globiformis Complexed with an inhibitor 8-Azaxanthine
Authors: Hossain, M.T. / Juan, E.C.M. / Suzuki, K. / Yamamoto, T. / Imamura, S. / Sekiguchi, T. / Takenaka, A.
History
DepositionFeb 19, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uric acid oxidase
B: Uric acid oxidase
C: Uric acid oxidase
D: Uric acid oxidase
E: Uric acid oxidase
F: Uric acid oxidase
G: Uric acid oxidase
H: Uric acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,88916
Polymers259,6648
Non-polymers1,2258
Water19,2041066
1
A: Uric acid oxidase
B: Uric acid oxidase
C: Uric acid oxidase
D: Uric acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,4458
Polymers129,8324
Non-polymers6124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24890 Å2
ΔGint-75 kcal/mol
Surface area39480 Å2
MethodPISA
2
E: Uric acid oxidase
F: Uric acid oxidase
G: Uric acid oxidase
H: Uric acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,4458
Polymers129,8324
Non-polymers6124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24860 Å2
ΔGint-78 kcal/mol
Surface area39420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.330, 122.280, 283.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer

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Components

#1: Protein
Uric acid oxidase / Uricase


Mass: 32458.027 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Arthrobacter globiformis (bacteria) / References: factor-independent urate hydroxylase
#2: Chemical
ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H3N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1066 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 9
Details: PEG 8000, Lithium sulphate, pH 9.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→20 Å / Num. all: 739628 / Num. obs: 132537 / % possible obs: 97.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.237 / % possible all: 87.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UOX

1uox
PDB Unreleased entry


Resolution: 2.24→20 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflectionSelection details
Rfree0.242 11837 Random
Rwork0.197 --
obs0.197 118345 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.8 Å20 Å20 Å2
2---2 Å20 Å2
3----13.79 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.24→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18256 0 88 1066 19410
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.68
LS refinement shellResolution: 2.24→2.32 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection% reflection
Rfree0.266 801 -
Rwork0.197 --
obs-7686 61.4 %

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