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- PDB-3pkf: Urate oxidase under 0.2 MPa / 2 bars pressure of equimolar mixtur... -

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Basic information

Entry
Database: PDB / ID: 3pkf
TitleUrate oxidase under 0.2 MPa / 2 bars pressure of equimolar mixture of xenon and nitrous oxide
ComponentsUricase
KeywordsOXIDOREDUCTASE / T-fold / Oxidase / Peroxisome / tetramer / uric acid degradation
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-AZAXANTHINE / XENON / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY / Resolution: 1.65 Å
AuthorsMarassio, G. / Colloc'h, N. / Prange, T. / Abraini, J.H.
CitationJournal: Faseb J. / Year: 2011
Title: Pressure-response analysis of anesthetic gases xenon and nitrous oxide on urate oxidase: a crystallographic study.
Authors: Marassio, G. / Prange, T. / David, H.N. / Sopkova-de Oliveira Santos, J. / Gabison, L. / Delcroix, N. / Abraini, J.H. / Colloc'h, N.
History
DepositionNov 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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_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.conn_type_id / _struct_conn.id / _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_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_conn.ptnr2_label_seq_id / _struct_conn_type.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 1.4Nov 27, 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)34,4914
Polymers34,1841
Non-polymers3073
Water3,639202
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,96416
Polymers136,7344
Non-polymers1,23012
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 area26740 Å2
ΔGint-162 kcal/mol
Surface area44490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.374, 96.302, 105.542
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-613-

HOH

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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-NA / SODIUM ION


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


Mass: 131.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Xe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growTemperature: 298 K / Method: batch / pH: 8.5
Details: 10-15 mg.ml-1 Urate oxidase, 2 mg/ml 8-azaxanthine, 50 mM Tris/HCl pH 8.5, 5-8 % PEG 8000, 0-0.05 M NaCl, BATCH, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2010 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 48685 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rsym value: 0.093 / Net I/σ(I): 12.6
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 5 / Rsym value: 0.327 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: RIGID BODY
Starting model: PDB entry 2IBA

2iba


Resolution: 1.65→19.76 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.449 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18121 2460 5.1 %RANDOM
Rwork0.16608 ---
obs0.16687 46152 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.149 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 13 202 2577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222458
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9343336
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50524.492118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40115435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2481513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211850
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8451.51474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64322407
X-RAY DIFFRACTIONr_scbond_it2.4523984
X-RAY DIFFRACTIONr_scangle_it4.2024.5928
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 172 -
Rwork0.262 3420 -
obs--99.67 %

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