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- PDB-2yzd: Crystal structure of uricase from Arthrobacter globiformis in com... -

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Basic information

Entry
Database: PDB / ID: 2yzd
TitleCrystal structure of uricase from Arthrobacter globiformis in complex with 8-azaxanthin (inhibitor)
ComponentsUricase
KeywordsOXIDOREDUCTASE / uricase / 8-azaxanthin
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / purine nucleobase metabolic process
Similarity search - Function
Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
8-AZAXANTHINE / Uricase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsJuan, E.C.M. / Hossain, M.T. / Hoque, M.M. / Suzuki, K. / Sekiguchi, T. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of Arthrobacter globiformis urate oxidase-ligand complexes.
Authors: Juan, E.C. / Hoque, M.M. / Shimizu, S. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Suzuki, K. / Tsunoda, M. / Amano, H. / Sekiguchi, T. / Takenaka, A.
History
DepositionMay 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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
Revision 1.3Aug 6, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uricase
B: Uricase
C: Uricase
D: Uricase
E: Uricase
F: Uricase
G: Uricase
H: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,43016
Polymers271,2058
Non-polymers1,2258
Water20,8971160
1
A: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,2158
Polymers135,6034
Non-polymers6124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24860 Å2
ΔGint-76.6 kcal/mol
Surface area39440 Å2
MethodPISA
2
E: Uricase
F: Uricase
G: Uricase
H: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,2158
Polymers135,6034
Non-polymers6124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24910 Å2
ΔGint-75.9 kcal/mol
Surface area39570 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

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Components

#1: Protein
Uricase


Mass: 33900.629 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Arthrobacter globiformis (bacteria)
References: UniProt: D0VWQ1*PLUS, 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.: 1160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsTHE SEQUENCE DATABASE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNP. IT WILL BE SUBMITTED TO UNP ...THE SEQUENCE DATABASE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNP. IT WILL BE SUBMITTED TO UNP DATABASE SOON.

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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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 8000, lithium sulfate, sodium borate buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, 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 12, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→20 Å / Num. obs: 132537 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 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
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
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. reflection% reflectionSelection details
Rfree0.2393 11841 -Random
Rwork0.1893 ---
all-139807 --
obs-118368 84.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.749 Å20 Å20 Å2
2--2.007 Å20 Å2
3----13.742 Å2
Refinement stepCycle: LAST / Resolution: 2.24→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18276 0 88 1160 19524

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