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- PDB-9qw5: Urate Oxidase from Aspergillus Flavus with its Inhibitor 9-Methyl... -

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Basic information

Entry
Database: PDB / ID: 9qw5
TitleUrate Oxidase from Aspergillus Flavus with its Inhibitor 9-Methyl Uric Acid by continuous serial electron diffraction (SerialED)
ComponentsUricase
KeywordsOXIDOREDUCTASE / serial electron diffraction / SerialED / UOX / MUA / Oxidase
Function / homology
Function and homology information


factor-independent urate hydroxylase / urate oxidase activity / purine nucleobase catabolic process / urate catabolic process / peroxisome
Similarity search - Function
Uricase, conserved site / Uricase signature. / Uricase / Uricase
Similarity search - Domain/homology
9-METHYL URIC ACID / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.25 Å
AuthorsHofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Scaletti Hutchinson, E. / Stenmark, P. / Di Palma, M. / Williams, L. / Worral, J. ...Hofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Scaletti Hutchinson, E. / Stenmark, P. / Di Palma, M. / Williams, L. / Worral, J. / Steiner, R. / Xu, H. / Zou, X.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Continuous Serial Electron Diffraction for High Quality Protein Structures
Authors: Hofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Williams, L. / Worrall, J. / Steiner, R. / Xu, H. / Zou, X.
History
DepositionApr 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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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)34,6693
Polymers34,3051
Non-polymers3642
Water7,692427
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,67612
Polymers137,2194
Non-polymers1,4578
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 area26140 Å2
ΔGint-72 kcal/mol
Surface area42120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.580, 94.490, 103.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Uricase / Rasburicase / Urate oxidase


Mass: 34304.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, Uox / Production host: Escherichia coli (E. coli)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-MUA / 9-METHYL URIC ACID


Mass: 182.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Uricase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.0345 MDa / Experimental value: NO
Source (natural)Organism: Aspergillus flavus (mold)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 22 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Dipped in 1% Tween-20 / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-1/1
VitrificationCryogen name: ETHANE / Details: Backside blotted and plunge frozen by hand

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / C2 aperture diameter: 20 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.05 sec. / Electron dose: 1.2 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Num. of diffraction images: 56538 / Num. of grids imaged: 1
EM diffraction shellResolution: 1.25→19.82 Å / Fourier space coverage: 99.96 % / Multiplicity: 225.95 / Num. of structure factors: 109263 / Phase residual: 17.4 °
EM diffraction statsFourier space coverage: 99.96 % / High resolution: 1.25 Å / Num. of intensities measured: 24688447 / Num. of structure factors: 109263 / Phase error rejection criteria: 0 / Rmerge: 0.127
ReflectionBiso Wilson estimate: 10.07 Å2

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Processing

EM software
IDNameCategory
6Cootmodel fitting
13PHENIXmodel refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 80.58 Å / B: 94.49 Å / C: 103.89 Å / Space group name: I222 / Space group num: 23
CTF correctionType: NONE
3D reconstructionResolution: 1.25 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER
Atomic model buildingPDB-ID: 4D12

4d12


Accession code: 4D12 / Source name: PDB / Type: experimental model
RefinementResolution: 1.25→17.49 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 1053 0.97 %
Rwork0.1913 108047 -
obs0.1914 109100 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.05 Å2
Refinement stepCycle: LAST / Resolution: 1.25→17.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 26 427 2819
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0112693
ELECTRON CRYSTALLOGRAPHYf_angle_d1.13701
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d12.514387
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.08410
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.008477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.310.40351230.371213307ELECTRON CRYSTALLOGRAPHY99
1.31-1.380.35261120.339213393ELECTRON CRYSTALLOGRAPHY100
1.38-1.460.30561480.294613389ELECTRON CRYSTALLOGRAPHY100
1.46-1.570.30481360.253913438ELECTRON CRYSTALLOGRAPHY100
1.57-1.730.21191230.208913486ELECTRON CRYSTALLOGRAPHY100
1.73-1.980.20391370.167313509ELECTRON CRYSTALLOGRAPHY100
1.98-2.50.17731210.151713607ELECTRON CRYSTALLOGRAPHY100
2.5-17.490.14361530.143213918ELECTRON CRYSTALLOGRAPHY100
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON CRYSTALLOGRAPHY

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44620.1775-0.94030.2125-0.28381.29380.10260.09220.1274-0.018-0.02550.0646-0.1684-0.1183-0.12280.16580.0188-0.0050.07370.01240.012431.926664.493539.7378
20.17170.02080.06170.0358-0.03550.0916-0.01880.06190.0695-0.07160.01040.0178-0.0489-0.0151-0.05810.20740.00280.00210.08190.0240.008336.013366.19133.3242
30.1294-0.02190.06390.19740.00570.2181-0.00170.0285-0.0004-0.0379-0.01310.0509-0.0111-0.0450.01620.1439-0.0038-0.01240.08550.00570.039523.633948.778942.108
42.8797-0.6876-1.41090.63620.76071.1295-0.056-0.0012-0.20210.03110.0237-0.00110.14730.010.0330.195-0.0052-0.01560.07510.00020.073732.689517.92939.3808
50.1799-0.00080.06530.2069-0.07690.31350.01010.0371-0.0144-0.05620.00850.06340.0305-0.0476-0.00060.15580.0019-0.01560.09210.0010.05722.783440.066436.1648
60.40540.11450.04970.31360.05671.28480.00820.0559-0.0413-0.0568-0.01560.03580.0629-0.0652-0.02080.1570.0095-0.01790.0715-0.02480.031929.014431.385739.8133
Refinement TLS group

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 26 )1 - 261 - 26
22chain 'A' and (resid 27 through 104 )27 - 10427 - 104
33chain 'A' and (resid 105 through 163 )105 - 163105 - 163
44chain 'A' and (resid 164 through 177 )164 - 177164 - 177
55chain 'A' and (resid 178 through 271 )178 - 271178 - 271
66chain 'A' and (resid 272 through 296 )272 - 296272 - 296

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