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- PDB-3l9g: Urate oxidase complexed with uric acid and chloride -

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Basic information

Entry
Database: PDB / ID: 3l9g
TitleUrate oxidase complexed with uric acid and chloride
ComponentsUricase
KeywordsOXIDOREDUCTASE / URATE OXIDASE / HIGH RESOLUTION / URIC ACID / ASPERGILLUS FLAVUS / Peroxisome / Purine metabolism
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
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsPrange, T. / Colloc'h, N. / Gabison, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand.
Authors: Gabison, L. / Chiadmi, M. / El Hajji, M. / Castro, B. / Colloc'h, N. / Prange, T.
#1: Journal: Febs Lett. / Year: 2006
Title: Recapture of [S]-allantoin, the product of the two-step degradation of uric acid, by urate oxidase.
Authors: Gabison, L. / Chiadmi, M. / Colloc'h, N. / Castro, B. / El Hajji, M. / Prange, T.
#2: Journal: Bmc Struct.Biol. / Year: 2008
Title: Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications.
Authors: Gabison, L. / Prange, T. / Colloc'h, N. / El Hajji, M. / Castro, B. / Chiadmi, M.
#3: Journal: Biophys.J. / Year: 2008
Title: Oxygen pressurized X-ray crystallography: probing the dioxygen binding site in cofactorless urate oxidase and implications for its catalytic mechanism.
Authors: Colloc'h, N. / Gabison, L. / Monard, G. / Altarsha, M. / Chiadmi, M. / Marassio, G. / Sopkova-de Oliveira Santos, J. / El Hajji, M. / Castro, B. / Abraini, J.H. / Prange, T.
History
DepositionJan 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Nov 1, 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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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)33,8695
Polymers33,5251
Non-polymers3454
Water4,468248
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,47820
Polymers134,0994
Non-polymers1,37916
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 area23840 Å2
ΔGint-126 kcal/mol
Surface area43760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.737, 94.941, 104.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uricase / Urate oxidase


Mass: 33524.758 Da / Num. of mol.: 1 / Fragment: UNP residues 2-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase

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Non-polymers , 5 types, 252 molecules

#2: Chemical ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 291 K / Method: batch / pH: 8
Details: 0.05M TRIS BUFFER PH 8, 8% PEG 8000, BATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.948 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 14, 2008 / Details: SI(111)
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 1.75→10.2 Å / Num. all: 41223 / Num. obs: 39071 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.7 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.053 / Net I/σ(I): 33.1
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3868 / Rsym value: 0.188 / % possible all: 99

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Processing

Software
NameClassification
DNAdata collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3L8W

3l8w


Resolution: 1.75→10 Å / Num. parameters: 10643 / Num. restraintsaints: 9920 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1883 -RANDOM
Rwork0.1751 ---
all0.184 41223 --
obs0.1794 39071 99.9 %-
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 2304.5 / Occupancy sum non hydrogen: 2627.5
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 22 248 2633
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.049
X-RAY DIFFRACTIONs_angle_d0.078
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0291
X-RAY DIFFRACTIONs_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.124
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0

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