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- PDB-3f2m: Urate oxidase complexed with 8-azaxanthine at 150 MPa -

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Basic information

Entry
Database: PDB / ID: 3f2m
TitleUrate oxidase complexed with 8-azaxanthine at 150 MPa
ComponentsUricase
KeywordsOXIDOREDUCTASE / HIGH PRESSURE / URIC ACID DEGRADATION / TETRAMER / T-FOLD DOMAIN / PEROXISOME / PURINE METABOLISM / HPMX
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 / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsColloc'h, N. / Girard, E. / Kahn, R. / Fourme, R.
CitationJournal: Biophys.J. / Year: 2010
Title: Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure.
Authors: Girard, E. / Marchal, S. / Perez, J. / Finet, S. / Kahn, R. / Fourme, R. / Marassio, G. / Dhaussy, A.C. / Prange, T. / Giffard, M. / Dulin, F. / Bonnete, F. / Lange, R. / Abraini, J.H. / ...Authors: Girard, E. / Marchal, S. / Perez, J. / Finet, S. / Kahn, R. / Fourme, R. / Marassio, G. / Dhaussy, A.C. / Prange, T. / Giffard, M. / Dulin, F. / Bonnete, F. / Lange, R. / Abraini, J.H. / Mezouar, M. / Colloc'h, N.
History
DepositionOct 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Sep 15, 2021Group: Database references / Derived calculations / Structure summary
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_keywords / 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 / _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_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 / _struct_keywords.text / _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 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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)34,3603
Polymers34,1841
Non-polymers1762
Water2,504139
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,43912
Polymers136,7344
Non-polymers7048
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 area25730 Å2
ΔGint-164 kcal/mol
Surface area43510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.700, 95.870, 104.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.2MG/ML URATE OXIDASE, EQUIMOLAR CONCENTRATION 8-AZAXANTHINE, 6% PEG 8000, 50mM Tris, 100mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID27 / Wavelength: 0.374 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 14, 2006 / Details: unfocused beam
RadiationMonochromator: SI (111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.374 Å / Relative weight: 1
ReflectionResolution: 1.8→19.936 Å / Num. all: 96518 / Num. obs: 36047 / % possible obs: 96.4 % / Observed criterion σ(I): 1.5 / Redundancy: 2.7 % / Biso Wilson estimate: 20.862 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 7.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.92.60.2622.51383152320.26296.6
1.9-2.012.60.1574.11300849690.15797.3
2.01-2.152.60.1054.31235946720.10596.8
2.15-2.322.70.07591163543740.07597
2.32-2.552.70.06310.61067040020.06396.5
2.55-2.852.70.05211.9963136080.05296.3
2.85-3.292.80.04313.7883532010.04396.1
3.29-4.022.80.04113.5753627060.04195.4
4.02-5.692.80.0414.2591621110.0495.1
5.69-19.942.60.04112.8309711720.04192.3

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Processing

Software
NameVersionClassificationNB
SCALA3.2.21data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
specdata collection
XDSdata reduction
REFMACphasing
RefinementStarting model: 2IBA

2iba


Resolution: 1.8→14.82 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.195 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.842 / SU B: 2.689 / SU ML: 0.081 / SU R Cruickshank DPI: 0.109 / SU Rfree: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: rigid body, HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1801 5 %RANDOM
Rwork0.182 ---
obs0.184 35998 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.3 Å2 / Biso mean: 24.534 Å2 / Biso min: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→14.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 12 139 2513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222433
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9343301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91624.561114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31815425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.3171512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021825
X-RAY DIFFRACTIONr_nbd_refined0.210.2940
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2127
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.227
X-RAY DIFFRACTIONr_mcbond_it0.9751.51471
X-RAY DIFFRACTIONr_mcangle_it1.8122395
X-RAY DIFFRACTIONr_scbond_it2.79331011
X-RAY DIFFRACTIONr_scangle_it4.6184.5906
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 138 -
Rwork0.28 2476 -
all-2614 -
obs--96.03 %

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