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

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Basic information

Entry
Database: PDB / ID: 2yzc
TitleCrystal structure of uricase from Arthrobacter globiformis in complex with allantoate
ComponentsUricase
KeywordsOXIDOREDUCTASE / uricase / allantoate
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
ALLANTOATE ION / Uricase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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

Downloads & links

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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)272,60616
Polymers271,2058
Non-polymers1,4018
Water35,8501990
1
A: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,3038
Polymers135,6034
Non-polymers7004
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25110 Å2
ΔGint-76.7 kcal/mol
Surface area39730 Å2
MethodPISA
2
E: Uricase
F: Uricase
G: Uricase
H: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,3038
Polymers135,6034
Non-polymers7004
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25200 Å2
ΔGint-76.3 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.498, 122.942, 284.784
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-1AL / ALLANTOATE ION / DIUREIDO-ACETATE


Mass: 175.123 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H7N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1990 / 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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG8000, lithium sulfate, sodium borate buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Oct 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 231814 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.236 / % possible all: 83.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1uox

1uox
PDB Unreleased entry


Resolution: 1.88→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.463 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.118 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19484 11617 5 %RANDOM
Rwork0.15938 ---
obs0.16117 220001 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.551 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2--0.04 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18248 0 96 1990 20334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02118760
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.91625456
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99152288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2730.22800
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214696
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.27933
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.21473
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3971.511384
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.648218272
X-RAY DIFFRACTIONr_scbond_it7.76637376
X-RAY DIFFRACTIONr_scangle_it10.0554.57184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.883→1.931 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 794
Rwork0.187 14539

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