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- PDB-6oe8: The crystal structure of hyper-thermostable AgUricase mutant K12C... -

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Basic information

Entry
Database: PDB / ID: 6oe8
TitleThe crystal structure of hyper-thermostable AgUricase mutant K12C/E286C
ComponentsUricase
KeywordsOXIDOREDUCTASE / Uricase / Arthrobacter globiformis / thermostability / disulfide cross-linking
Function / homology
Function and homology information


purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome
Similarity search - Function
Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / TRIETHYLENE GLYCOL / Uricase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsShi, Y. / Wang, T. / Zhou, X.E. / Liu, Q. / Jiang, Y. / Xu, H.E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770796 China
CitationJournal: Acta Pharmacol.Sin. / Year: 2019
Title: Structure-based design of a hyperthermostable AgUricase for hyperuricemia and gout therapy.
Authors: Shi, Y. / Wang, T. / Zhou, X.E. / Liu, Q.F. / Jiang, Y. / Xu, H.E.
History
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,43525
Polymers146,4474
Non-polymers2,98921
Water22,1041227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33740 Å2
ΔGint-7 kcal/mol
Surface area37300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.932, 149.105, 84.956
Angle α, β, γ (deg.)90.00, 118.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-705-

HOH

21A-709-

HOH

31B-719-

HOH

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Components

#1: Protein
Uricase / Urate oxidase / AgUOX


Mass: 36611.648 Da / Num. of mol.: 4 / Mutation: K12C, E286C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: uox / Production host: Escherichia coli (E. coli)
References: UniProt: D0VWQ1, factor-independent urate hydroxylase
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1227 / 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: 2.54 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 12% (w/v) polyethylene glycol 3350 and 0.1M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→40 Å / Num. obs: 97576 / % possible obs: 97.4 % / Redundancy: 3.4 % / CC1/2: 0.983 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.4
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.308 / Num. unique obs: 9744 / CC1/2: 0.922 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YZB

2yzb


Resolution: 1.99→37.276 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 1998 2.05 %
Rwork0.18 --
obs0.1806 97457 97.46 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→37.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9489 0 0 1227 10716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059684
X-RAY DIFFRACTIONf_angle_d0.87813079
X-RAY DIFFRACTIONf_dihedral_angle_d9.3335647
X-RAY DIFFRACTIONf_chiral_restr0.0591412
X-RAY DIFFRACTIONf_plane_restr0.0071716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9901-2.03980.27361380.21776614X-RAY DIFFRACTION94
2.0398-2.0950.24361450.20156876X-RAY DIFFRACTION98
2.095-2.15660.21881380.19656699X-RAY DIFFRACTION97
2.1566-2.22620.25681410.19246720X-RAY DIFFRACTION96
2.2262-2.30580.22081430.19336872X-RAY DIFFRACTION99
2.3058-2.39810.24951450.19376891X-RAY DIFFRACTION99
2.3981-2.50720.24421440.19596864X-RAY DIFFRACTION98
2.5072-2.63930.21431450.19246929X-RAY DIFFRACTION99
2.6393-2.80470.19031390.18586673X-RAY DIFFRACTION96
2.8047-3.02110.2031440.18446875X-RAY DIFFRACTION98
3.0211-3.3250.20871450.18586919X-RAY DIFFRACTION99
3.325-3.80570.18241450.1696894X-RAY DIFFRACTION99
3.8057-4.79320.17141410.1456759X-RAY DIFFRACTION96
4.7932-37.28280.19031450.17476874X-RAY DIFFRACTION97

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