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- PDB-4n3m: Joint neutron/X-ray structure of urate oxidase in complex with 8-... -

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Basic information

Entry
Database: PDB / ID: 4n3m
TitleJoint neutron/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)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / Resolution: 1.919 Å
AuthorsOksanen, E. / Blakeley, M.P. / Budayova-Spano, M.
CitationJournal: 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.
History
DepositionOct 7, 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 / Refinement description
Category: diffrn_detector / diffrn_radiation ...diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / refine / refine_ls_shell
Item: _diffrn_detector.details / _diffrn_detector.pdbx_collection_date ..._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.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_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.pdbx_refine_id / _refine_ls_shell.percent_reflns_obs

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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)34,3954
Polymers34,1841
Non-polymers2123
Water3,045169
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,58116
Polymers136,7344
Non-polymers84612
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 area23440 Å2
ΔGint-164 kcal/mol
Surface area41820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.200, 96.200, 105.500
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-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3N5O2
#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.: 169 / Source method: isolated from a natural source / Formula: D2O

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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: 58.71 %
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 REACTOROTHER23.25-4.35
Detector
TypeIDDetectorDateDetails
MAR scanner 345 mm plate1IMAGE PLATEApr 28, 2008Xenocs
CUSTOM-MADE2IMAGE PLATEAug 30, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Multilayer mirrorSINGLE WAVELENGTHMx-ray1
2Ni/Ti wavelength filterLAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
23.251
34.351
Reflection

Entry-ID: 4N3M

Resolution (Å)Num. allNum. obs% possible obs (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.9-61.43233622336273.20.14119.2
1.92-5096.50.042219.88
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-20.2362.6145.2
1.92-2.040.1448.53284.2

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Processing

Software
NameVersionClassification
LADI-IIIsoftwaredata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
LAUEGENdata reduction
SCALAdata scaling
Refinement

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)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)FOM work R setSU MLDiffraction-IDσ(F)Phase error
1.919-33.029X-RAY DIFFRACTION6624.4111.820.17230.13980.141415192886130380596.250.79830.1411.9916.44
1.904-48.1NEUTRON DIFFRACTION0.26720.23980.24121139231994.9171.820
Refinement stepCycle: LAST / Resolution: 1.904→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 13 169 2491
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0144983
NEUTRON DIFFRACTIONf_angle_d1.4858588
NEUTRON DIFFRACTIONf_dihedral_angle_d19.4321290
NEUTRON DIFFRACTIONf_chiral_restr0.104367
NEUTRON DIFFRACTIONf_plane_restr0.008805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9191-1.98770.24841180.1872234X-RAY DIFFRACTION76
1.9877-2.06730.21981530.15722910X-RAY DIFFRACTION98
2.0673-2.16140.16551540.1432932X-RAY DIFFRACTION99
2.1614-2.27530.18441550.14072928X-RAY DIFFRACTION99
2.2753-2.41780.18071550.14422945X-RAY DIFFRACTION99
2.4178-2.60440.19271560.15192973X-RAY DIFFRACTION100
2.6044-2.86640.20821570.15592980X-RAY DIFFRACTION100
2.8664-3.28080.19061590.14843010X-RAY DIFFRACTION100
3.2808-4.13220.14041580.12213022X-RAY DIFFRACTION100
4.1322-33.03380.13381540.12042927X-RAY DIFFRACTION93
1.9038-1.99050.3628830.36631586NEUTRON DIFFRACTION42
1.9905-2.09540.34161010.32952027NEUTRON DIFFRACTION53
2.0954-2.22670.31761220.2982307NEUTRON DIFFRACTION61
2.2267-2.39860.33871470.27242582NEUTRON DIFFRACTION68
2.3986-2.640.30081500.24582936NEUTRON DIFFRACTION77
2.64-3.0220.28221690.23173203NEUTRON DIFFRACTION84
3.022-3.80710.22751720.20633555NEUTRON DIFFRACTION92
3.8071-48.11530.20521950.19743864NEUTRON DIFFRACTION96

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