[English] 日本語
Yorodumi
- PDB-6ia9: urate oxidase under 2000 bar (220 MPa) of argon -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ia9
Titleurate oxidase under 2000 bar (220 MPa) of argon
ComponentsUricase
KeywordsOXIDOREDUCTASE / aspergillus flavus / homotetramer / purine metabolism / argon / high pressure
Function / homology
Function and homology information


purine nucleobase catabolic process / urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / peroxisome
Similarity search - Function
Uricase, conserved site / Uricase signature. / Uricase / Uricase
Similarity search - Domain/homology
ACETYL GROUP / ARGON / 8-AZAXANTHINE / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 2.0Sep 23, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_peptide_omega / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_type.scat_Cromer_Mann_a1 / _atom_type.scat_Cromer_Mann_a2 ..._atom_type.scat_Cromer_Mann_a1 / _atom_type.scat_Cromer_Mann_a2 / _atom_type.scat_Cromer_Mann_a3 / _atom_type.scat_Cromer_Mann_a4 / _atom_type.scat_Cromer_Mann_b1 / _atom_type.scat_Cromer_Mann_b2 / _atom_type.scat_Cromer_Mann_b3 / _atom_type.scat_Cromer_Mann_b4 / _atom_type.scat_Cromer_Mann_c / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _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_asym_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_mean / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _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_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.pdbx_R_Free_selection_details / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_method_to_determine_struct / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _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_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.number_obs / _software.name / _software.version / _struct_conf.beg_auth_asym_id / _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.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness
Details: The N-term acetyl group were not modelled in the initial deposition. Done now
Provider: author / Type: Coordinate replacement
Revision 3.0Feb 9, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / database_2 / entity / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_peptide_omega / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct / struct_asym / struct_conn / struct_mon_prot_cis
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_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 / _pdbx_validate_peptide_omega.omega / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_starting_model / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_all / _refine_ls_shell.pdbx_fsc_free / _refine_ls_shell.pdbx_fsc_work / _refine_ls_shell.wR_factor_R_work / _software.version / _struct.title / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model completeness
Details: This entry adopts the sorting of catalyric water molecules asked by one referee of the forthcoming paper. Please note that in the ligand AZA you are using for comparisons, an ideal angle C2- ...Details: This entry adopts the sorting of catalyric water molecules asked by one referee of the forthcoming paper. Please note that in the ligand AZA you are using for comparisons, an ideal angle C2-N1-C6 whic is probably erroneous (should be close to 123 deg, not equal to 115,.. deg.)
Provider: author / Type: Coordinate replacement
Revision 3.1Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
aaa: Uricase
aba: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,90414
Polymers66,9972
Non-polymers90612
Water8,845491
1
aaa: Uricase
aba: Uricase
hetero molecules

aaa: Uricase
aba: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,80728
Polymers133,9954
Non-polymers1,81324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area28460 Å2
ΔGint-148 kcal/mol
Surface area42880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.552, 96.682, 105.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 2 molecules aaaaba

#1: Protein Uricase / Urate oxidase


Mass: 33498.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Komagataella pastoris (fungus)
References: UniProt: Q00511, factor-independent urate hydroxylase

-
Non-polymers , 5 types, 503 molecules

#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-AR / ARGON


Mass: 39.948 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ar
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.5 % / Description: LARGE COLORLESS PRISMS
Crystal growTemperature: 291 K / Method: batch mode / pH: 8
Details: 20 microliter of protein (15 mg/ml) mixed with 20 microliter of solution: Buffer Tris 0.05M (chloride free) + 4% PEG 4000.

-
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: May 10, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 1.723→71.322 Å / Num. obs: 72278 / % possible obs: 93.8 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.017 / Rrim(I) all: 0.062 / Net I/σ(I): 22.8
Reflection shellResolution: 1.723→1.826 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2 / Num. unique obs: 3531 / CC1/2: 0.802 / Rpim(I) all: 0.26 / Rrim(I) all: 0.63 / % possible all: 56.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1r56 reconstructed dimer

1r56


Resolution: 1.8→46.333 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.014 / SU ML: 0.115 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.126 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2432 3583 4.957 %
Rwork0.209 68695 -
all0.211 --
obs-72278 96.208 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.255 Å2
Baniso -1Baniso -2Baniso -3
1--0.004 Å20 Å2-0 Å2
2--0.003 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4718 0 56 491 5265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124962
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.6386739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1925606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70122.93256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1215871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6031525
X-RAY DIFFRACTIONr_chiral_restr0.1160.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023765
X-RAY DIFFRACTIONr_nbd_refined0.220.22332
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23329
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2404
X-RAY DIFFRACTIONr_metal_ion_refined0.340.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.2130
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.238
X-RAY DIFFRACTIONr_mcbond_it4.0213.2692396
X-RAY DIFFRACTIONr_mcangle_it4.7554.8863000
X-RAY DIFFRACTIONr_scbond_it4.8363.4572566
X-RAY DIFFRACTIONr_scangle_it5.9415.0643733
X-RAY DIFFRACTIONr_lrange_it6.92144.5117815
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3921700.38634020.38654540.5730.54165.49320.349
1.847-1.8970.3422060.36142670.3653520.6850.66483.57620.329
1.897-1.9520.3262390.30649110.30752060.7720.77598.92430.263
1.952-2.0120.3152630.26547940.26750570.8330.8551000.227
2.012-2.0780.3042510.26646520.26849060.8450.86199.93890.225
2.078-2.1510.2982490.24145120.24447610.8660.8861000.207
2.151-2.2320.3032360.23943370.24245740.8690.88899.97810.213
2.232-2.3230.2842070.23342020.23544100.8960.90299.97730.205
2.323-2.4260.2931940.24740510.24942510.8650.88599.85890.222
2.426-2.5440.2792030.21538680.21840720.9060.91799.97540.2
2.544-2.6810.2482060.20636700.20938770.9110.92699.97420.192
2.681-2.8430.2812010.20634640.2136680.9050.92799.91820.199
2.843-3.0380.2651610.2233260.22234870.8920.9121000.218
3.038-3.2810.2661220.22530970.22632200.9130.92599.96890.225
3.281-3.5920.2231610.21228290.21229910.9480.94499.96660.218
3.592-4.0130.1881580.17725590.17827190.9580.96399.92640.188
4.013-4.6280.1781230.13523000.13724250.9710.97799.91750.15
4.628-5.6540.1621080.1419560.14120640.9740.9771000.156
5.654-7.9370.244810.18615530.18916340.9560.9711000.2
7.937-46.3330.187440.1829470.1829940.9790.97699.69820.214

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more