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- PDB-2fub: Crystal structure of urate oxidase at 140 MPa -

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Basic information

Entry
Database: PDB / ID: 2fub
TitleCrystal structure of urate oxidase at 140 MPa
ComponentsUricase
KeywordsOXIDOREDUCTASE / TETRAMER / HIGH PRESSURE / 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 / CYSTEINE / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY / Resolution: 2.3 Å
AuthorsColloc'h, N. / Girard, E. / Fourme, R.
CitationJournal: Biochim.Biophys.Acta / Year: 2006
Title: High pressure macromolecular crystallography: The 140-MPa crystal structure at 2.3 A resolution of urate oxidase, a 135-kDa tetrameric assembly
Authors: Colloc'h, N. / Girard, E. / Dhaussy, A.-C. / Kahn, R. / Ascone, I. / Mezouar, M. / Fourme, R.
History
DepositionJan 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 15, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_keywords / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_keywords.text / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id / _struct_conn_type.id
Revision 1.6Oct 30, 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)34,4323
Polymers34,1581
Non-polymers2742
Water1,982110
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,72712
Polymers136,6304
Non-polymers1,0978
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 area24580 Å2
ΔGint-107 kcal/mol
Surface area43370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.18, 95.63, 104.65
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsFunctionnal tetramer generated by the two fold axis 1-x , 1-y, z ; x, 1-y, 1-z ; 1-x, y, 1-z ;

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Components

#1: Protein Uricase / Urate oxidase


Mass: 34157.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus flavus (mold)
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-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350(6-10%), 50-100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.331 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 2004 / Details: UNFOCUSED BEAM
RadiationMonochromator: SI (111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.331 Å / Relative weight: 1
ReflectionResolution: 2.3→22.9 Å / Num. obs: 17696 / % possible obs: 97.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 30.94 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 9.2
Reflection shellResolution: 2.29→2.42 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2476 / Rsym value: 0.255 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: RIGID BODY
Starting model: PDB ENTRY 1R51

1r51


Resolution: 2.3→22.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.029 / SU ML: 0.144 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.232 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21342 894 5.1 %RANDOM
Rwork0.16136 ---
obs0.16412 16712 97.85 %-
all-17696 --
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 mean: 27.108 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→22.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 15 110 2484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222444
X-RAY DIFFRACTIONr_angle_refined_deg2.0711.9323314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8345294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.37424.359117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.05515427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8631514
X-RAY DIFFRACTIONr_chiral_restr0.1330.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021839
X-RAY DIFFRACTIONr_nbd_refined0.2190.2991
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21651
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.221
X-RAY DIFFRACTIONr_mcbond_it1.4621.51516
X-RAY DIFFRACTIONr_mcangle_it2.38822393
X-RAY DIFFRACTIONr_scbond_it3.54331087
X-RAY DIFFRACTIONr_scangle_it5.5134.5921
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 64 -
Rwork0.209 1208 -
obs--98.68 %

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