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- PDB-6i9z: urate oxidase under 65 bar of argon -

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Basic information

Entry
Database: PDB / ID: 6i9z
Titleurate oxidase under 65 bar of argon
ComponentsUricase
KeywordsOXIDOREDUCTASE / aspergillus flavus / homotetramer / purine metabolism / argon / high pressure
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
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. / Carpentier, P.
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 6, 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
Water3,981221
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 area26620 Å2
ΔGint-165 kcal/mol
Surface area44050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.323, 96.121, 105.412
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-NA / SODIUM ION


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


Mass: 39.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ar
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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→20 Å / Num. obs: 52954 / % possible obs: 98 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5301 / % possible all: 99.5

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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→14.32 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.673 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18296 2707 5.1 %RANDOM
Rwork0.15558 ---
obs0.15702 50192 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.744 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.6→14.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 13 221 2596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132454
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172222
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.6443322
X-RAY DIFFRACTIONr_angle_other_deg2.4131.5775180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1175294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23823.192130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05415435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.321512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02503
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_it2.3832.3051181
X-RAY DIFFRACTIONr_mcbond_other2.3842.3011180
X-RAY DIFFRACTIONr_mcangle_it3.3283.4531474
X-RAY DIFFRACTIONr_mcangle_other3.3283.4571475
X-RAY DIFFRACTIONr_scbond_it3.8862.7481273
X-RAY DIFFRACTIONr_scbond_other3.8852.7471274
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.863.9271848
X-RAY DIFFRACTIONr_long_range_B_refined7.06927.4692680
X-RAY DIFFRACTIONr_long_range_B_other7.01827.172656
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
Rfree0.305 173 -
Rwork0.3 3714 -
obs--99.46 %

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