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- PDB-2yze: Crystal structure of uricase from Arthrobacter globiformis -

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Basic information

Entry
Database: PDB / ID: 2yze
TitleCrystal structure of uricase from Arthrobacter globiformis
ComponentsUricase
KeywordsOXIDOREDUCTASE / uricase
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
(dihydroxyboranyloxy-hydroxy-boranyl)oxylithium / Uricase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsJuan, E.C.M. / Hossain, M.T. / Hoque, M.M. / Suzuki, K. / Sekiguchi, T. / Takenaka, A.
CitationJournal: To be Published
Title: Trapping of the uric acid substrate in the crystal structure of urate oxidase from Arthrobacter globiformis
Authors: Juan, E.C.M. / Hossain, M.T. / Hoque, M.M. / Yamamoto, T. / Imamura, S. / Suzuki, K. / 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

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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)272,09816
Polymers271,2058
Non-polymers8938
Water33,1301839
1
A: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0498
Polymers135,6034
Non-polymers4464
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24910 Å2
ΔGint-84.4 kcal/mol
Surface area39520 Å2
MethodPISA
2
E: Uricase
F: Uricase
G: Uricase
H: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0498
Polymers135,6034
Non-polymers4464
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24960 Å2
ΔGint-86.5 kcal/mol
Surface area39370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.430, 122.540, 284.460
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-NOB / (dihydroxyboranyloxy-hydroxy-boranyl)oxylithium


Mass: 111.584 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: B2H3LiO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1839 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 55.18 %
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 17, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→42.22 Å / Num. obs: 193433 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.47 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 3.34 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 4.7 / % possible all: 87.1

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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: 1.99→10 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 18946 -Random
Rwork0.1914 ---
all-202860 --
obs-190430 93.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.4 Å20 Å20 Å2
2--1.61 Å20 Å2
3---5.79 Å2
Refinement stepCycle: LAST / Resolution: 1.99→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18247 0 64 1839 20150

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