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- PDB-1vax: Crystal Structure of Uricase from Arthrobacter globiformis -

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Basic information

Entry
Database: PDB / ID: 1vax
TitleCrystal Structure of Uricase from Arthrobacter globiformis
ComponentsUric acid oxidaseUrate oxidase
KeywordsOXIDOREDUCTASE
Function / homologyUrate Oxidase / Urate Oxidase; / Roll / Alpha Beta
Function and homology information
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)259,6648
Polymers259,6648
Non-polymers00
Water33,8501879
1
A: Uric acid oxidase
B: Uric acid oxidase
C: Uric acid oxidase
D: Uric acid oxidase


Theoretical massNumber of molelcules
Total (without water)129,8324
Polymers129,8324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23330 Å2
ΔGint-90 kcal/mol
Surface area40050 Å2
MethodPISA
2
E: Uric acid oxidase
F: Uric acid oxidase
G: Uric acid oxidase
H: Uric acid oxidase


Theoretical massNumber of molelcules
Total (without water)129,8324
Polymers129,8324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23440 Å2
ΔGint-90 kcal/mol
Surface area39820 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
DetailsThe biological assembly is a tetramer

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Components

#1: Protein
Uric acid oxidase / Urate 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1879 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
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 17, 2003
RadiationProtocol: 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. all: 1260560 / Num. obs: 363070 / % possible obs: 91.8 % / Redundancy: 3.47 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.3
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
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
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
Rfree0.223 18946 -Random
Rwork0.193 ---
obs0.193 190429 93.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.41 Å20 Å20 Å2
2---1.66 Å20 Å2
3----5.75 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.99→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18256 0 0 1879 20135
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shellResolution: 1.99→2.06 Å / Rfactor Rfree error: 0.006
RfactorNum. reflection% reflection
Rfree0.249 1770 -
Rwork0.21 --
obs-16137 89.3 %

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