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- PDB-6rgt: Crystal structure of the cofactor-free Aspergillus flavus urate o... -

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Basic information

Entry
Database: PDB / ID: 6rgt
TitleCrystal structure of the cofactor-free Aspergillus flavus urate oxidase T57A variant anaerobically complexed with 9-methyl uric acid
ComponentsUricase
KeywordsOXIDOREDUCTASE / COFACTOR-FREE OXIDASE / COMPLEX
Function / homology
Function and homology information


purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / 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
9-METHYL URIC ACID / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsBui, S. / Lowden, S.R.J. / Steiner, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/P000169/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the cofactor-free Aspergillus flavus urate oxidase T57A variant anaerobically complexed with 9-methyl uric acid
Authors: Bui, S. / Lowden, S.R.J. / Steiner, R.A.
History
DepositionApr 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,8035
Polymers34,2591
Non-polymers5454
Water10,755597
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,21320
Polymers137,0354
Non-polymers2,17816
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 area27540 Å2
ΔGint-82 kcal/mol
Surface area47090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.291, 95.116, 104.503
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-1048-

HOH

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Components

#1: Protein Uricase / Urate oxidase


Mass: 34258.719 Da / Num. of mol.: 1 / Mutation: T57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-MUA / 9-METHYL URIC ACID


Mass: 182.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4O3
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 20 MG/ML UOX T57A IN 50 MM TRIS-HCL PH 8.0 SATURATED WITH 9-METHYL URIC ACID, 8% PEG 8000 - CRYSTALS GROWN ANAEROBICALLY

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→14.02 Å / Num. obs: 52248 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.051 / Rrim(I) all: 0.117 / Net I/σ(I): 9.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3 % / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7601 / CC1/2: 0.361 / Rpim(I) all: 0.991 / Rrim(I) all: 1.738 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4CW0

4cw0


Resolution: 1.6→14.02 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.294 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18905 2683 5.1 %RANDOM
Rwork0.16152 ---
obs0.16295 49561 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.011 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2---0.57 Å20 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 1.6→14.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 37 597 3038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132764
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172539
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.6483793
X-RAY DIFFRACTIONr_angle_other_deg1.4591.5865949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1665364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08923.197147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63415503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7051515
X-RAY DIFFRACTIONr_chiral_restr0.080.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023202
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02575
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_it1.8411.5121318
X-RAY DIFFRACTIONr_mcbond_other1.8151.5011315
X-RAY DIFFRACTIONr_mcangle_it2.9032.2451668
X-RAY DIFFRACTIONr_mcangle_other2.9032.2531669
X-RAY DIFFRACTIONr_scbond_it2.0531.6861446
X-RAY DIFFRACTIONr_scbond_other2.0531.6891447
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2722.4432105
X-RAY DIFFRACTIONr_long_range_B_refined7.66319.9623334
X-RAY DIFFRACTIONr_long_range_B_other6.4917.963104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 204 -
Rwork0.355 3605 -
obs--99.14 %

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