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- PDB-6rgm: urate oxidase under 130 bar of krypton -

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Basic information

Entry
Database: PDB / ID: 6rgm
Titleurate oxidase under 130 bar of krypton
ComponentsUricase
KeywordsOXIDOREDUCTASE / aspergillus flavus / homotetramer / purine metabolism / krypton / 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
Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 8-AZAXANTHINE / KRYPTON / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsPrange, T. / Colloc'h, N. / Carpentier, P.
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
DepositionApr 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / refine / struct_conn
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 / _refine.pdbx_diffrn_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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)35,14312
Polymers34,1841
Non-polymers95911
Water9,206511
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,57148
Polymers136,7344
Non-polymers3,83744
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 area33250 Å2
ΔGint-261 kcal/mol
Surface area43090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.250, 94.940, 104.080
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-1604-

HOH

21A-1672-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uricase / Urate oxidase


Mass: 34183.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The last five residues not observed / Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase

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Non-polymers , 6 types, 522 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3N5O2
#5: Chemical ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Kr
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.97 Å3/Da / Density % sol: 58.5 % / Description: Diamond shape crystals
Crystal growTemperature: 291 K / Method: batch mode / pH: 8
Details: 20 microliters of protein+azaxanthin, pH 8 TRIS 0.05M mixed with 20 microliters TRIS 0.05M + 10 % (v:v) PEG 8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 1.5→70.14 Å / Num. obs: 62225 / % possible obs: 99.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.017 / Net I/σ(I): 21.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 8901 / Rpim(I) all: 0.21 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
cctbx.xfeldata reduction
XSCALEdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6IC1

6ic1


Resolution: 1.5→70.14 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.113 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16949 3146 5.1 %RANDOM
Rwork0.14031 ---
obs0.14177 59041 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.257 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→70.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 51 511 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132568
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172366
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.6493489
X-RAY DIFFRACTIONr_angle_other_deg1.5381.585511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4585317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26622.782133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34115457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2881513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022853
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02528
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9421.971227
X-RAY DIFFRACTIONr_mcbond_other1.9021.9621224
X-RAY DIFFRACTIONr_mcangle_it2.8162.9491538
X-RAY DIFFRACTIONr_mcangle_other2.8152.9541539
X-RAY DIFFRACTIONr_scbond_it3.2492.3041341
X-RAY DIFFRACTIONr_scbond_other3.2482.3031342
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7983.3211944
X-RAY DIFFRACTIONr_long_range_B_refined7.4727.2293120
X-RAY DIFFRACTIONr_long_range_B_other6.76324.7112912
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 241 -
Rwork0.271 4307 -
obs--99.8 %

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