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- PDB-9qw6: Urate Oxidase from Aspergillus Flavus with its Substrate Uric Aci... -

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Basic information

Entry
Database: PDB / ID: 9qw6
TitleUrate Oxidase from Aspergillus Flavus with its Substrate Uric Acid by continuous serial electron diffraction (SerialED)
ComponentsUricase
KeywordsOXIDOREDUCTASE / serial electron diffraction / SerialED / UOX / UA / 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
OXYGEN MOLECULE / URIC ACID / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.75 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)34,4893
Polymers34,2891
Non-polymers2002
Water6,125340
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,95512
Polymers137,1554
Non-polymers8008
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 area25240 Å2
ΔGint-124 kcal/mol
Surface area42860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.130, 94.440, 103.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Urate oxidase


Mass: 34288.742 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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#3: Chemical ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 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: Manually back side blotted and plunge frozen

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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: 2.2 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Num. of diffraction images: 3823 / Num. of grids imaged: 1
EM diffraction shellResolution: 1.75→26.38 Å / Fourier space coverage: 96.93 % / Multiplicity: 20.61 / Num. of structure factors: 38877 / Phase residual: 21.56 °
EM diffraction statsFourier space coverage: 96.93 % / High resolution: 1.75 Å / Num. of intensities measured: 801293 / Num. of structure factors: 38877 / Phase error rejection criteria: 0 / Rmerge: 0.219
ReflectionBiso Wilson estimate: 13.62 Å2

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Processing

EM software
IDNameCategory
6Cootmodel fitting
8PHENIXmolecular replacement
13PHENIXmodel refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 80.13 Å / B: 94.44 Å / C: 103.97 Å / Space group name: I222 / Space group num: 23
CTF correctionType: NONE
3D reconstructionResolution: 1.75 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingPDB-ID: 4D12

4d12


Pdb chain-ID: A / Accession code: 4D12 / Source name: PDB / Type: experimental model
RefinementResolution: 1.75→17.48 Å / SU ML: 0.2524 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 962 2.49 %
Rwork0.2205 37745 -
obs0.2211 38707 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.45 Å2
Refinement stepCycle: LAST / Resolution: 1.75→17.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 14 340 2719
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00642652
ELECTRON CRYSTALLOGRAPHYf_angle_d0.63763636
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0488406
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0042468
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d5.5932377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.840.36471340.33225244ELECTRON CRYSTALLOGRAPHY95.03
1.84-1.960.28651340.28695255ELECTRON CRYSTALLOGRAPHY95.48
1.96-2.110.27911350.24725313ELECTRON CRYSTALLOGRAPHY95.9
2.11-2.320.24371360.23145348ELECTRON CRYSTALLOGRAPHY96.63
2.32-2.650.27011380.22515413ELECTRON CRYSTALLOGRAPHY97.32
2.65-3.340.22391390.20185490ELECTRON CRYSTALLOGRAPHY97.71
3.34-17.480.19411460.17755682ELECTRON CRYSTALLOGRAPHY98.26
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)
11.379232201780.248294885544-0.5091422705840.425693811758-0.1728262776691.0735796570.06457997979970.1088164076550.161361052972-0.0769014752231-0.005333847274820.0599834574036-0.0434937172955-0.12689736639-0.03050672559860.1055910291550.0107818606394-0.003040536575710.07014630909490.03662913823510.10782300125331.627808402364.574478526839.6637799894
20.7119734739440.0833286380039-0.03530722711820.269331828459-0.09144671141460.196740985335-0.04361053404460.1345641983220.0295975241966-0.1008451229210.03270636038060.0258763353509-0.0651814001968-0.02337916614810.00399862988390.1369204793610.002132959840450.003499953205450.1121767360150.01374508334650.096284537966935.454739970166.407350166633.4192723975
30.3442717341240.0718766237430.04166518392120.7018034368380.158231114641.08292495251-0.0444596291910.0205217679095-0.03969424095060.0116466516318-0.02065317280060.06129652996260.0897354476128-0.06874705677730.04283566771210.08502497433570.00659792844329-0.01748313796740.1143773748870.01910226180410.11366118188722.941669647655.583608365142.502142848
40.304585188485-0.08427899706010.0364474821890.432984157394-0.2470390373440.326385445061-0.0008496906472870.0247778693329-0.04519301535-0.026910957230.04761454368580.1216297185520.00349514559194-0.0559281623022-0.03024872647820.133857954923-0.00342171913167-0.02598656088590.135444715122-0.01250539521070.11159253971822.803306076437.270636872834.8067892502
50.632260020963-0.1959098821530.2336144044940.853051470749-0.4572914910161.12671037520.01788402061570.0621662934165-0.0633599175696-0.1182186872360.004742998968030.04623689473160.21076069986-0.043231139457-0.04004422647190.125398237723-0.00445525463502-0.006065622882970.095703158357-0.01530955196890.099417084789728.152699244430.599073670942.1232878638
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 147 )105 - 147105 - 147
44chain 'A' and (resid 148 through 241 )148 - 241148 - 241
55chain 'A' and (resid 242 through 296 )242 - 296242 - 296

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