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- PDB-4n9s: High resolution X-RAY STRUCTURE OF URATE OXIDASE IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 4n9s
TitleHigh resolution X-RAY STRUCTURE OF URATE OXIDASE IN COMPLEX WITH 8-HYDROXYXANTHINE
ComponentsUricase
KeywordsOXIDOREDUCTASE / urate oxidase / uricase
Function / homology
Function and homology information


purine nucleobase catabolic process / urate oxidase activity / factor-independent urate hydroxylase / 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
8-hydroxy-3,9-dihydro-1H-purine-2,6-dione / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsOksanen, E. / Blakeley, M.P. / Budayova-Spano, M.
Citation
Journal: Plos One / Year: 2014
Title: The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation.
Authors: Oksanen, E. / Blakeley, M.P. / El-Hajji, M. / Ryde, U. / Budayova-Spano, M.
#1: Journal: J. R. Soc. Interface / Year: 2009
Title: Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Sep 20, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5025
Polymers34,1841
Non-polymers3194
Water8,503472
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,00920
Polymers136,7344
Non-polymers1,27516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area24800 Å2
ΔGint-155 kcal/mol
Surface area42090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.930, 95.370, 104.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uricase / Urate oxidase


Mass: 34183.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase

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Non-polymers , 5 types, 476 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-8HX / 8-hydroxy-3,9-dihydro-1H-purine-2,6-dione / 8-hydroxyxanthine


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 5 % PEG 8000, 0.1 M NACL, 0.1 M TRISHCL PD 8.5, 8 MG/ML URATE OXIDASE, temperature-controlled batch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 14, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.06→50 Å / Num. all: 176905 / Num. obs: 176905 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.037 / Net I/σ(I): 15.71
Reflection shellResolution: 1.06→1.09 Å / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 2.77 / Num. unique all: 11052 / % possible all: 87

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IBA

2iba


Resolution: 1.06→35.269 Å / SU ML: 0.11 / σ(F): 1.99 / Phase error: 12.34 / Stereochemistry target values: ML
Details: EXPLICIT HYDROGENS DERIVED FROM THE NEUTRON STRUCTURE WERE USED IN RIDING POSITIONS IN THIS STRUCTURE, AND PROBABLY THESE RESIDUES HAVE DIFFERENT LEUCINE ROTAMERS (A194 AND A244) THAN IN THE NEUTRON STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1414 8903 5.03 %5% random
Rwork0.1257 ---
all0.1265 176940 --
obs0.1265 176940 98.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.311 Å2 / ksol: 0.424 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8374 Å2-0 Å2-0 Å2
2---3.2254 Å20 Å2
3----0.982 Å2
Refinement stepCycle: LAST / Resolution: 1.06→35.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 20 472 2839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072574
X-RAY DIFFRACTIONf_angle_d1.3783524
X-RAY DIFFRACTIONf_dihedral_angle_d15.736954
X-RAY DIFFRACTIONf_chiral_restr0.131396
X-RAY DIFFRACTIONf_plane_restr0.006450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0604-1.09830.22187710.203914833X-RAY DIFFRACTION87
1.0983-1.14230.17239220.149216856X-RAY DIFFRACTION100
1.1423-1.19430.14349180.124316874X-RAY DIFFRACTION100
1.1943-1.25730.13578890.113916925X-RAY DIFFRACTION100
1.2573-1.3360.12858790.103917037X-RAY DIFFRACTION100
1.336-1.43920.11749020.097716966X-RAY DIFFRACTION100
1.4392-1.5840.11568970.088717069X-RAY DIFFRACTION100
1.584-1.81320.10968930.090917129X-RAY DIFFRACTION100
1.8132-2.28440.11788740.106517078X-RAY DIFFRACTION99
2.2844-35.28880.14979580.140417270X-RAY DIFFRACTION98

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