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- PDB-1r4s: URATE OXIDASE FROM ASPERGILLUS FLAVUS COMPLEXED WITH ITS INHIBITO... -

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Basic information

Entry
Database: PDB / ID: 1r4s
TitleURATE OXIDASE FROM ASPERGILLUS FLAVUS COMPLEXED WITH ITS INHIBITOR 9-METHYL URIC ACID
ComponentsUricase
KeywordsOXIDOREDUCTASE / URIC ACID DEGRADATION / DIMERIC BARREL / TUNNEL-SHAPED PROTEIN
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
CYSTEINE / 9-METHYL URIC ACID / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRetailleau, P. / Colloc'h, N. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Complexed and ligand-free high-resolution structures of urate oxidase (Uox) from Aspergillus flavus: a reassignment of the active-site binding mode.
Authors: Retailleau, P. / Colloc'h, N. / Vivares, D. / Bonnete, F. / Castro, B. / El-Hajji, M. / Mornon, J.P. / Monard, G. / Prange, T.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal Structure of the Protein Drug Urate Oxidase-Inhibitor Complex at 2.05 A Resolution
Authors: Colloc'h, N. / El Hajji, M. / Bachet, B. / L'Hermite, G. / Schiltz, M. / Prange, T. / Castro, B. / Mornon, J.-P.
History
DepositionOct 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 28, 2014Group: Non-polymer description
Revision 1.4Feb 28, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 23, 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 / struct_conn / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 13, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._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_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

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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)34,5033
Polymers34,2001
Non-polymers3032
Water4,161231
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,01212
Polymers136,7984
Non-polymers1,2138
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 area25950 Å2
ΔGint-106 kcal/mol
Surface area44100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.083, 96.460, 105.674
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: 34199.586 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-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-MUA / 9-METHYL URIC ACID


Mass: 182.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8.5MG/ML PROTEIN, 0.2MG/ML 9-METHYL URIC ACID, 5-7% W/V PEG 8000, 100MM TRIS/HCL, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97 / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
20.9721
ReflectionResolution: 1.8→20 Å / Num. obs: 38023 / % possible obs: 100 % / Redundancy: 9 % / Rsym value: 0.072 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.245 / % possible all: 99.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UOX

1uox
PDB Unreleased entry


Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.182 2376 RANDOM
Rwork0.154 --
all0.157 --
obs-38023 -
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 16 231 2610
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.22
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_dihedral_angle_d17.3

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