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- PDB-6ia3: urate oxidase under 220 bar (22 MPa) of argon -

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Basic information

Entry
Database: PDB / ID: 6ia3
Titleurate oxidase under 220 bar (22 MPa) of argon
ComponentsUricaseUrate oxidase
KeywordsOXIDOREDUCTASE / aspergillus flavus / homotetramer / purine metabolism / argon / high pressure
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / purine nucleobase metabolic process / peroxisome
Similarity search - Function
Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
ARGON / 8-AZAXANTHINE / PHOSPHATE ION / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 Å
AuthorsPrange, T. / Colloc'h, N. / Carpentier, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Acta Cryst. D / Year: 2022
Title: Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization
Authors: Prange, T. / Carpentier, P. / Dhaussy, A.C. / Girard, E. / Colloc'h, N.
#1: Journal: Current trends in X-ray crystallography / Year: 2011
Title: Current trends in X-ray Crystallography. Intech Open books
Authors: Colloc'h, N. / Marassio, G. / Prange, T.
#2: Journal: Journal of Applied Crystallography / Year: 2016
Title: Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel soak-and-freeze methodology
Authors: Lafumat, B. / Mueller-Dieckmann, C. / Leonard, G. / Colloc'h, N. / Prange, T. / Giraud, T. / Dobias, F. / Royant, A. / van der Linden, P. / Carpentier, P.
History
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 2.0Feb 9, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / database_2 / diffrn_radiation / entity / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation.monochromator / _pdbx_contact_author.fax / _pdbx_contact_author.id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[2][2] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_starting_model / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_all / _software.version / _struct.title / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model completeness
Details: The problem was a mainly: -Finalizing some residue refinements and -Re-ordering water molecules as to correspond with those of equivalent structures, in particular 6ia9; with the catalytic ...Details: The problem was a mainly: -Finalizing some residue refinements and -Re-ordering water molecules as to correspond with those of equivalent structures, in particular 6ia9; with the catalytic water in 1st position for a given chain, followed by the waters of the 'proton shuttle', as described in the corresponding paper
Provider: author / Type: Coordinate replacement
Revision 2.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)34,7718
Polymers34,1841
Non-polymers5877
Water8,143452
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,08432
Polymers136,7344
Non-polymers2,34928
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 area28240 Å2
ΔGint-187 kcal/mol
Surface area42450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.787, 95.149, 104.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1554-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uricase / Urate oxidase / Urate oxidase


Mass: 34183.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The 6 LAST RESIDUES AT THE C-Terminus NOT OBSERVED IN THE EXPERIMENTAL DENSITY. THE ACE (Acetate) GROUP AT N-Terminus IS PART OF THE PROTEIN, NOT COMING FROM THE EXPRESSION SYSTEM
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Saccharomyces (fungus)
References: UniProt: Q00511, factor-independent urate hydroxylase

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Non-polymers , 6 types, 459 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-AR / ARGON / Argon


Mass: 39.948 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ar
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 57.5 % / Description: LARGE COLORLESS PRISMS
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.5
Details: 20 microliter of protein (15 mg/ml) mixed with 20 microliter of solution: buffer (Tris 0.05M /Phosphate 0.05M) + 4% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.77 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 1.69→70 Å / Num. obs: 39125 / % possible obs: 87.8 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.016 / Net I/σ(I): 31.3
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.172 / Num. unique obs: 2310 / Rpim(I) all: 0.116 / % possible all: 36.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2IBA

2iba


Resolution: 1.69→47.62 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.658 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 1831 4.7 %RANDOM
Rwork0.1478 ---
obs0.1494 37292 87.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.77 Å2 / Biso mean: 13.696 Å2 / Biso min: 6.57 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.69→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 37 454 2853
Biso mean--17.88 25.36 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132536
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152365
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.6483445
X-RAY DIFFRACTIONr_angle_other_deg1.4551.5855468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6135312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21823.168131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92815448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4461512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022861
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02575
LS refinement shellResolution: 1.692→1.736 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.722 34 -
Rwork0.697 668 -
all-702 -
obs--21.56 %

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