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- PDB-7a0l: Joint neutron/X-ray room temperature structure of perdeuterated A... -

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Basic information

Entry
Database: PDB / ID: 7a0l
TitleJoint neutron/X-ray room temperature structure of perdeuterated Aspergillus flavus urate oxidase in complex with the 8-azaxanthine inhibitor and catalytic water bound in the peroxo hole
ComponentsUricase
KeywordsOXIDOREDUCTASE / COFACTOR-FREE OXIDASE / INHIBITOR / CATALYTIC WATER / DIOXYGEN BINDING
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / purine nucleobase catabolic process / urate catabolic process / peroxisome
Similarity search - Function
Uricase, conserved site / Uricase signature. / Uricase / Uricase
Similarity search - Domain/homology
8-AZAXANTHINE / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMcGregor, L. / Bui, S. / Blakeley, M.P. / Steiner, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P000169/1 United Kingdom
CitationJournal: Iucrj / Year: 2021
Title: Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis.
Authors: McGregor, L. / Foldes, T. / Bui, S. / Moulin, M. / Coquelle, N. / Blakeley, M.P. / Rosta, E. / Steiner, R.A.
History
DepositionAug 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)34,4653
Polymers34,2891
Non-polymers1762
Water6,323351
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,85912
Polymers137,1554
Non-polymers7048
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 area26620 Å2
ΔGint-44 kcal/mol
Surface area42850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.628, 96.130, 105.397
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
Components on special symmetry positions
IDModelComponents
11A-827-

HOH

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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-AZA / 8-AZAXANTHINE


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


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


Mass: 18.015 Da / Num. of mol.: 351 / 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

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.6 / Details: TRIS-Acetate, PEG 8000, 8AZA

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
NUCLEAR REACTORILL LADI III13.12-4.20
SYNCHROTRONESRF BM30A20.98
Detector
TypeIDDetectorDate
LADI III1IMAGE PLATEOct 30, 2018
ADSC QUANTUM 315r2CCDOct 30, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
13.121
24.21
30.981
Reflection

Biso Wilson estimate: 16.6 Å2 / Entry-ID: 7A0L

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.1-401923480.23.40.9870.1410.07915.8
1.33-52.79364399.89.210.0410.014224.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
2.1-2.213.30.3832.923570.8260.215168.1
1.33-1.355.31.27345050.4650.598296.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
LAUEGENdata processing
DIALSdata processing
SCALAdata scaling
PHENIXphasing
xia2data reduction
Refinement
Method to determine structureStarting modelResolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLDiffraction-IDCross valid methodσ(F)Phase errorShrinkage radii (Å)VDW probe radii (Å)Stereochemistry target valuesSolvent model
MOLECULAR REPLACEMENT4D12

4d12

1.33-35.51X-RAY DIFFRACTION24.170.10930.10160.10196749174631936433.7299.720.11882FREE R-VALUE0.3111.77570.91.11GeoStd + Monomer Library + CDL v1.2FLAT BULK SOLVENT MODEL
MOLECULAR REPLACEMENT4D12

4d12

2.1-32.21NEUTRON DIFFRACTION0.23030.21471908078.660.11881FREE R-VALUE11.77570.91.11GeoStd + Monomer Library + CDL v1.2FLAT BULK SOLVENT MODEL
X-RAY+NEUTRON
Refinement stepCycle: LAST / Resolution: 1.33→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 12 351 2729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY+NEUTRONf_bond_d0.00985885
X-RAY+NEUTRONf_angle_d1.41110013
X-RAY+NEUTRONf_chiral_restr0.0915416
X-RAY+NEUTRONf_plane_restr0.0064817
X-RAY+NEUTRONf_dihedral_angle_d18.62391567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.350.31542230.31325672X-RAY+NEUTRON95.99
1.35-1.360.31842340.2955718X-RAY+NEUTRON98.82
1.36-1.380.32532130.28415802X-RAY+NEUTRON99.18
1.38-1.390.27792410.26485809X-RAY+NEUTRON99.77
1.39-1.410.26022000.23215877X-RAY+NEUTRON99.79
1.41-1.430.19972500.19365795X-RAY+NEUTRON99.85
1.43-1.450.19311830.18225789X-RAY+NEUTRON99.87
1.45-1.470.18062260.16575847X-RAY+NEUTRON99.92
1.47-1.50.14812180.15425827X-RAY+NEUTRON99.97
1.5-1.520.15062190.13765866X-RAY+NEUTRON99.82
1.52-1.550.14072460.13095841X-RAY+NEUTRON99.89
1.55-1.580.11841970.11775868X-RAY+NEUTRON99.92
1.58-1.610.11472540.10645788X-RAY+NEUTRON99.95
1.61-1.640.09672220.09575838X-RAY+NEUTRON99.93
1.64-1.680.11342580.09925776X-RAY+NEUTRON99.97
1.68-1.710.11232130.09355870X-RAY+NEUTRON99.97
1.71-1.760.09922330.08275777X-RAY+NEUTRON99.93
1.76-1.80.10522090.07945855X-RAY+NEUTRON99.97
1.81-1.860.09732120.07635867X-RAY+NEUTRON99.93
1.86-1.920.09752280.07475827X-RAY+NEUTRON99.9
1.92-1.990.07392200.07035811X-RAY+NEUTRON99.93
1.99-2.070.08362600.0725846X-RAY+NEUTRON99.89
2.07-2.160.09082040.07735844X-RAY+NEUTRON100
2.16-2.270.08442000.07875856X-RAY+NEUTRON99.98
2.27-2.420.11172030.08515874X-RAY+NEUTRON99.97
2.42-2.60.10232190.09135839X-RAY+NEUTRON99.98
2.6-2.860.10482500.09995781X-RAY+NEUTRON99.95
2.86-3.280.11122620.1045809X-RAY+NEUTRON99.9
3.28-4.130.08282360.08785815X-RAY+NEUTRON99.84
4.13-35.510.09792160.09765847X-RAY+NEUTRON99.85

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