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- PDB-6i9x: urate oxidase under 35 bar of argon -

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Basic information

Entry
Database: PDB / ID: 6i9x
Titleurate oxidase under 35 bar of argon
ComponentsUricase
KeywordsOXIDOREDUCTASE / aspergillus flavus / homotetramer / purine metabolism / argon / high pressure
Function / homology
Function and homology information


urate oxidase activity / purine nucleobase catabolic process / 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
ARGON / 8-AZAXANTHINE / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsPrange, T. / Colloc'h, N.
Citation
Journal: Acta Cryst. D / Year: 2022
Title: Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization
Authors: Prange, T. / Carpentier, P. / Dhaussy, A.C. / Girard, E. / Colloc'h, N.
#1: Journal: Current trends in X-ray crystallography / Year: 2011
Title: Protein-noble gas interactions investigated by crystallography on three enzymes - Implication on anesthesia and neuroprotection mechanism.
Authors: Colloc'h, N. / Marassio, G. / Prange, T.
#2: Journal: J. Applied Crystallography / Year: 2016
Title: Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel 'soak-and-freeze' methodology
Authors: Lafumat, B. / Mueller-Dieckmann, C. / Leonard, G. / Colloc'h, N. / Prange, T. / Giraud, T. / Dobbias, F. / Royant, R. / van der Linden, P. / Carpentier, P.
History
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)34,4004
Polymers34,1841
Non-polymers2163
Water4,125229
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,59916
Polymers136,7344
Non-polymers86412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area26490 Å2
ΔGint-161 kcal/mol
Surface area44120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.234, 96.114, 105.389
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
Details: 6 RESIDUES AT THE C-END NOT OBSERVED IN THE DENSITY: SER-LEU-LYS-SER-LYS-LEU 296- ..... ...-301
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-AR / ARGON


Mass: 39.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ar
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
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: 57.5 % / Description: LARGE COLORLESS PRISMS
Crystal growTemperature: 291 K / Method: batch mode / pH: 8
Details: 20 microliter of protein (15 mg/ml) mixed with 20 microliter of solution: Tris 0.05M (chloride free) + 4% PEG 4000.

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9775 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2005
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.6→14.78 Å / Num. obs: 53681 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 18.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.226 / Num. unique obs: 5277 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
SCALEPACKdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1R51

1r51


Resolution: 1.6→14.78 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.315 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.066 / Details: HYDROGENS HAVE BEEN USED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17832 2729 5.1 %RANDOM
Rwork0.15051 ---
obs0.1519 50892 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.568 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.6→14.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 13 229 2604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132447
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172222
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.6433318
X-RAY DIFFRACTIONr_angle_other_deg2.1761.5775178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9155294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96323.14129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09615434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6171512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022713
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02503
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3532.2751181
X-RAY DIFFRACTIONr_mcbond_other2.3512.2711180
X-RAY DIFFRACTIONr_mcangle_it3.3363.4131474
X-RAY DIFFRACTIONr_mcangle_other3.3383.4171475
X-RAY DIFFRACTIONr_scbond_it4.0372.7121266
X-RAY DIFFRACTIONr_scbond_other4.0352.7111267
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1033.8791844
X-RAY DIFFRACTIONr_long_range_B_refined7.15327.1692684
X-RAY DIFFRACTIONr_long_range_B_other7.10726.8592660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 187 -
Rwork0.206 3677 -
obs--99.69 %

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