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- PDB-4n9v: High resolution x-ray structure of urate oxidase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4n9v
TitleHigh resolution x-ray structure of urate oxidase in complex with 8-azaxanthine
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-AZAXANTHINE / DEUTERATED WATER / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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.
Authors: Oksanen, E. / Blakeley, M.P. / Bonnete, F. / Dauvergne, M.T. / Dauvergne, F. / Budayova-Spano, M.
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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 1.3Nov 6, 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)34,9249
Polymers34,1841
Non-polymers7418
Water9,584532
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,69736
Polymers136,7344
Non-polymers2,96332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area24760 Å2
ΔGint-153 kcal/mol
Surface area41290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.800, 95.080, 104.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-774-

DOD

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uricase / Aspergillus flavus urate oxidase / 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 , 6 types, 540 molecules

#2: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H3N5O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: D2O

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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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 5 % PEG 8000, 0.1 M NACL, 0.1M 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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 4, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. all: 158812 / Num. obs: 158812 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.94
Reflection shellResolution: 1.1→1.13 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.93 / % possible all: 99.7

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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: 1.1→35.162 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 13.83 / 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 (A244 AND A268) THAN IN THE NEUTRON STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1532 7940 5 %5% random
Rwork0.1389 ---
all0.1396 158797 --
obs0.1396 158797 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.618 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1316 Å2-0 Å2-0 Å2
2---2.0845 Å20 Å2
3----2.7607 Å2
Refinement stepCycle: LAST / Resolution: 1.1→35.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 43 532 2918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082595
X-RAY DIFFRACTIONf_angle_d1.373565
X-RAY DIFFRACTIONf_dihedral_angle_d15.912947
X-RAY DIFFRACTIONf_chiral_restr0.133396
X-RAY DIFFRACTIONf_plane_restr0.007457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.13930.19257940.195415084X-RAY DIFFRACTION100
1.1393-1.18490.1877890.163614985X-RAY DIFFRACTION100
1.1849-1.23890.15737930.150815063X-RAY DIFFRACTION100
1.2389-1.30420.15987920.137715046X-RAY DIFFRACTION100
1.3042-1.38590.14827910.12615031X-RAY DIFFRACTION99
1.3859-1.49290.14967930.118715065X-RAY DIFFRACTION99
1.4929-1.64310.13387880.113414982X-RAY DIFFRACTION99
1.6431-1.88090.13657900.117215005X-RAY DIFFRACTION98
1.8809-2.36970.12787930.117815063X-RAY DIFFRACTION98
2.3697-35.17980.15668170.145715533X-RAY DIFFRACTION99

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