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- PDB-5frc: Structure of urate oxidase prepared by the 'soak-and-freeze' meth... -

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Basic information

Entry
Database: PDB / ID: 5frc
TitleStructure of urate oxidase prepared by the 'soak-and-freeze' method under 42 bar of oxygen pressure
ComponentsURICASE
KeywordsOXIDOREDUCTASE / URATE OXIDASE / DIOXYGEN / PRESSURE / FLASH FREEZING
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
8-AZAXANTHINE / OXYGEN MOLECULE / Uricase
Similarity search - Component
Biological speciesASPERGILLUS FLAVUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.443 Å
AuthorsLafumat, B. / Mueller-Dieckmann, C. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P.
CitationJournal: J.Appl.Crystallogr. / 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. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P.
History
DepositionDec 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Structure summary
Revision 1.2Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Jun 27, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_atom_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_atom_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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: URICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3924
Polymers34,1841
Non-polymers2083
Water6,666370
1
A: URICASE
hetero molecules

A: URICASE
hetero molecules

A: URICASE
hetero molecules

A: URICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,56716
Polymers136,7344
Non-polymers83212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation2_655-x+1,-y,z1
Buried area26280 Å2
ΔGint-146.7 kcal/mol
Surface area42960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.898, 95.351, 104.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2146-

HOH

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Components

#1: Protein URICASE / URATE OXIDASE


Mass: 34183.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: URATE OXIDASE AND 8-AZAXANTHINE FROZEN UNDER 42BAR O2
Source: (gene. exp.) ASPERGILLUS FLAVUS (mold) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3N5O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.95 Å3/Da / Density % sol: 58.34 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.44→47.68 Å / Num. obs: 70982 / % possible obs: 97.5 % / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Biso Wilson estimate: 19.97 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.5
Reflection shellResolution: 1.44→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 1.5 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XDSXSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PO6

4po6


Resolution: 1.443→47.675 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 16.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1648 3481 4.9 %
Rwork0.1415 --
obs0.1427 70982 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.443→47.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 14 370 2746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062534
X-RAY DIFFRACTIONf_angle_d1.0723451
X-RAY DIFFRACTIONf_dihedral_angle_d14.064934
X-RAY DIFFRACTIONf_chiral_restr0.041381
X-RAY DIFFRACTIONf_plane_restr0.004444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.443-1.46280.25991290.23392071X-RAY DIFFRACTION77
1.4628-1.48370.32271380.2612725X-RAY DIFFRACTION99
1.4837-1.50580.25681320.20412752X-RAY DIFFRACTION100
1.5058-1.52930.2351410.20992696X-RAY DIFFRACTION99
1.5293-1.55440.22121390.16952734X-RAY DIFFRACTION100
1.5544-1.58120.22581380.15532733X-RAY DIFFRACTION100
1.5812-1.610.18241460.14132734X-RAY DIFFRACTION100
1.61-1.64090.18561470.14132723X-RAY DIFFRACTION100
1.6409-1.67440.17321250.1332771X-RAY DIFFRACTION99
1.6744-1.71080.15851580.12432707X-RAY DIFFRACTION100
1.7108-1.75060.16871340.11952748X-RAY DIFFRACTION100
1.7506-1.79440.16831380.122736X-RAY DIFFRACTION100
1.7944-1.84290.15651430.13082752X-RAY DIFFRACTION100
1.8429-1.89720.20321380.14822716X-RAY DIFFRACTION98
1.8972-1.95840.22661140.18172543X-RAY DIFFRACTION93
1.9584-2.02840.1621460.12432749X-RAY DIFFRACTION99
2.0284-2.10960.13691340.12192663X-RAY DIFFRACTION97
2.1096-2.20560.12711240.12772786X-RAY DIFFRACTION99
2.2056-2.32190.22421440.16282585X-RAY DIFFRACTION93
2.3219-2.46740.17291330.14222750X-RAY DIFFRACTION99
2.4674-2.65790.16771560.14292720X-RAY DIFFRACTION98
2.6579-2.92530.17881440.14592731X-RAY DIFFRACTION97
2.9253-3.34850.14211490.14112744X-RAY DIFFRACTION98
3.3485-4.21840.14541400.12982752X-RAY DIFFRACTION97
4.2184-47.70150.13771510.13542880X-RAY DIFFRACTION97

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