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- PDB-3ld4: Urate oxidase complexed with 8-nitro xanthine -

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Basic information

Entry
Database: PDB / ID: 3ld4
TitleUrate oxidase complexed with 8-nitro xanthine
ComponentsUricase
KeywordsOXIDOREDUCTASE / URATE OXIDASE / ASPERGILLUS FLAVUS / NITROXANTHINE / THIOXANTHINE / XANTHINE / PROTONATION / Peroxisome / Purine metabolism
Function / homology
Function and homology information


urate oxidase activity / purine nucleobase catabolic process / 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-nitro-3,7-dihydro-1H-purine-2,6-dione / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.35 Å
AuthorsPrange, T. / Colloc'h, N. / Gabison, L.
CitationJournal: 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.
History
DepositionJan 12, 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 1.3Feb 28, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Nov 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 1.5Nov 20, 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)33,8074
Polymers33,5251
Non-polymers2823
Water4,774265
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,22816
Polymers134,0994
Non-polymers1,12912
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 area23800 Å2
ΔGint-121 kcal/mol
Surface area44170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.582, 95.045, 104.371
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: 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
#2: Chemical ChemComp-8NX / 8-nitro-3,7-dihydro-1H-purine-2,6-dione / 8-nitro xanthine


Mass: 197.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H3N5O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 291 K / Method: batch / pH: 8
Details: 0.05M TRIS BUFFER PH 8, 8% PEG 8000, 0.02M NACL , BATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.964 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2007 / Details: CURVATED MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.35→29.4 Å / Num. all: 87363 / Num. obs: 81256 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 7.6 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.044 / Net I/σ(I): 25
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 4.4 / Num. unique all: 11863 / Rsym value: 0.16 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: 3L8W

3l8w


Resolution: 1.35→10 Å / Num. parameters: 10727 / Num. restraintsaints: 9947 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3978 -RANDOM
Rwork0.182 ---
all0.192 85679 --
obs0.185 80616 99.4 %-
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 2313 / Occupancy sum non hydrogen: 2648.5
Refinement stepCycle: LAST / Resolution: 1.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 19 265 2647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.027
X-RAY DIFFRACTIONs_angle_d0.072
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0301
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.074
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0

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