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- PDB-4n9m: Joint neutron/x-ray structure of urate oxidase in complex with 8-... -

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Basic information

Entry
Database: PDB / ID: 4n9m
TitleJoint neutron/x-ray structure of urate oxidase in complex with 8-hydroxyxanthine
ComponentsUricase
KeywordsOXIDOREDUCTASE / urate oxidase / uricase oxidoreductase
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / purine nucleobase catabolic process / 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 / DEUTERATED WATER / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.023 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 1.2Jun 13, 2018Group: Data collection / Database references / Refinement description
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / refine / refine_ls_shell / reflns / reflns_shell
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _diffrn_detector.details / _diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_FOM_work_R_set / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_refine_id / _refine.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_refine_id / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.number_all / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _refine_hist.d_res_low / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4104
Polymers34,1841
Non-polymers2273
Water3,369187
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,64116
Polymers136,7344
Non-polymers90612
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 area24500 Å2
ΔGint-163 kcal/mol
Surface area42050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.180, 96.260, 105.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#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
#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 291 K / Method: temperature-controlled batch / 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

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceTypeIDWavelength (Å)
SEALED TUBEOTHER11.54
NUCLEAR REACTOROTHER23.25-4.15
Detector
TypeIDDetectorDateDetails
MAR scanner 345 mm plate1IMAGE PLATEOct 28, 2008Xenocs
CUSTOM-MADE2IMAGE PLATEAug 30, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1multilayer mirrorSINGLE WAVELENGTHMx-ray1
2Ni/Ti multilayer filterLAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
23.251
34.151
Reflection

Entry-ID: 4N9M

Resolution (Å)Num. allNum. obs% possible obs (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2-2098.50.04123.56
2.3-40.06131791317972.20.13327.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-IDNum. unique all% possible all
2-2.140.1459.541
2.3-2.420.192.22132850.6

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Processing

Software
NameVersionClassification
LADI-IIIsoftwaredata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
LAUEGENdata reduction
SCALAdata scaling
Refinement

Baniso 12: 0 Å2 / Baniso 13: 0 Å2 / Baniso 23: -0 Å2 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Baniso 11 (Å2)Baniso 22 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)FOM work R setSU MLDiffraction-IDσ(F)Phase errorBsol (Å2)ksol (e/Å3)
2.023-19.209X-RAY DIFFRACTION75.119.132.5915.74235.50131.36150.18870.16660.167813172502726344597.640.75730.2111.9919.4325.0070.365
2.298-40.067NEUTRON DIFFRACTION14.55847.90636.46840.28840.25860.2601663131745.0371.0820200.6
Refinement stepCycle: LAST / Resolution: 2.023→19.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 14 187 2529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0755246
X-RAY DIFFRACTIONf_angle_d2.4098830
X-RAY DIFFRACTIONf_chiral_restr0.048374
X-RAY DIFFRACTIONf_plane_restr0.002738
X-RAY DIFFRACTIONf_dihedral_angle_d16.2751337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
2.0231-2.1040.30581220.22862311X-RAY DIFFRACTION2433981
2.104-2.19960.19831450.1962775X-RAY DIFFRACTION29209100
2.1996-2.31540.22681490.19052807X-RAY DIFFRACTION29569100
2.3154-2.46020.24321480.18962821X-RAY DIFFRACTION29699100
2.4602-2.64970.2111490.1852831X-RAY DIFFRACTION29809100
2.6497-2.91550.21071490.18612842X-RAY DIFFRACTION29919100
2.9155-3.33550.1981500.17362833X-RAY DIFFRACTION29839100
3.3355-4.19510.16461510.14292864X-RAY DIFFRACTION30159100
4.1951-19.20970.13141540.13452943X-RAY DIFFRACTION3097998
2.3-2.47560.4472910.36221754NEUTRON DIFFRACTION1845551
2.4756-2.72470.317980.32691985NEUTRON DIFFRACTION2083557
2.7247-3.11880.36651300.29052370NEUTRON DIFFRACTION2500568
3.1188-3.92880.29011650.23252983NEUTRON DIFFRACTION3148585
3.9288-40.07320.20951790.21783419NEUTRON DIFFRACTION3598593

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