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- PDB-8rtr: Bilirubin oxidase from Myrothecium verrucaria with R356S mutation -

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Basic information

Entry
Database: PDB / ID: 8rtr
TitleBilirubin oxidase from Myrothecium verrucaria with R356S mutation
ComponentsBilirubin oxidase
KeywordsOXIDOREDUCTASE / Trp-His cross link / mutant
Function / homology
Function and homology information


bilirubin oxidase activity / bilirubin oxidase / copper ion binding
Similarity search - Function
Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / MALONIC ACID / OXYGEN MOLECULE / TRIETHYLENE GLYCOL / Bilirubin oxidase
Similarity search - Component
Biological speciesAlbifimbria verrucaria (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSvecova, L. / Koval, T. / Kolenko, P. / Ostergaard, L.H. / Dohnalek, J.
Funding support Czech Republic, European Union, 3items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447European Union
Czech Academy of Sciences86652036 Czech Republic
CitationJournal: To be published
Title: Bilirubin oxidase - answers to questions on ligand binding and Trp-His covalent link formation
Authors: Svecova, L. / Koval, T. / Kolenko, P. / Ostergaard, L.H. / Dohnalek, J.
History
DepositionJan 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Bilirubin oxidase
BBB: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,30439
Polymers119,8792
Non-polymers4,42537
Water20,8971160
1
AAA: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,48723
Polymers59,9401
Non-polymers2,54722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,81716
Polymers59,9401
Non-polymers1,87715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.072, 200.888, 217.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Bilirubin oxidase


Mass: 59939.570 Da / Num. of mol.: 2 / Mutation: R356S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Albifimbria verrucaria (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: Q12737, bilirubin oxidase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 7 types, 1193 molecules

#4: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1160 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.1 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 2.5
Details: 20% (w/v) PEG 3350, 0.1 M malonic acid pH 2.5, protein concentration 10 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.05→47.785 Å / Num. obs: 91634 / % possible obs: 99 % / Observed criterion σ(I): -3.7 / Redundancy: 5.3 % / Biso Wilson estimate: 23.6 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.106 / Rrim(I) all: 0.249 / Net I/σ(I): 7
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.715 / Mean I/σ(I) obs: 1 / Num. unique obs: 4539 / CC1/2: 0.387 / Rpim(I) all: 0.802 / Rrim(I) all: 1.899 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→47.785 Å / Cor.coef. Fo:Fc: 0.968 / SU B: 4.04 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.145
Details: Hydrogens have been added in their riding positions. The last refinement cycle was performed against all measured reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 4479 4.9 %RANDOM SELECTION
Rwork0.1581 91631 --
all0.16 ---
obs0.1598 91631 98.923 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.477 Å2-0 Å2-0 Å2
2---0.203 Å2-0 Å2
3----0.274 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8466 0 255 1160 9881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139094
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158123
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.67512457
X-RAY DIFFRACTIONr_angle_other_deg1.3251.59118739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.81151105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82222.074511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.492151294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9481560
X-RAY DIFFRACTIONr_chiral_restr0.0760.21182
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022193
X-RAY DIFFRACTIONr_nbd_refined0.2030.21672
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.27867
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24275
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.24084
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2857
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1170.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.224
X-RAY DIFFRACTIONr_nbd_other0.2050.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.222
X-RAY DIFFRACTIONr_mcbond_it1.7742.6384304
X-RAY DIFFRACTIONr_mcbond_other1.7742.6384303
X-RAY DIFFRACTIONr_mcangle_it2.5533.9555387
X-RAY DIFFRACTIONr_mcangle_other2.5523.9565388
X-RAY DIFFRACTIONr_scbond_it2.6222.9334788
X-RAY DIFFRACTIONr_scbond_other2.6082.9324787
X-RAY DIFFRACTIONr_scangle_it3.9584.3147048
X-RAY DIFFRACTIONr_scangle_other3.9584.3147049
X-RAY DIFFRACTIONr_lrange_it5.33332.17510263
X-RAY DIFFRACTIONr_lrange_other5.14231.5149969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.1030.293550.2846381X-RAY DIFFRACTION99.867
2.103-2.1610.2763030.2726366X-RAY DIFFRACTION99.955
2.161-2.2230.3032670.2466132X-RAY DIFFRACTION99.797
2.223-2.2910.2653180.2275929X-RAY DIFFRACTION99.348
2.291-2.3660.2563360.2085701X-RAY DIFFRACTION99.917
2.366-2.4490.2383010.25564X-RAY DIFFRACTION99.847
2.449-2.5410.2292710.1835387X-RAY DIFFRACTION99.859
2.541-2.6450.2143100.1685186X-RAY DIFFRACTION99.891
2.645-2.7620.232730.1624912X-RAY DIFFRACTION99.444
2.762-2.8960.2022500.1414740X-RAY DIFFRACTION99.462
2.896-3.0530.1922430.1274540X-RAY DIFFRACTION99.875
3.053-3.2370.1842270.1324271X-RAY DIFFRACTION99.823
3.237-3.4590.1751790.1314097X-RAY DIFFRACTION99.813
3.459-3.7350.1621780.1283742X-RAY DIFFRACTION99.015
3.735-4.0890.1411390.1132854X-RAY DIFFRACTION81.398
4.089-4.5670.1561440.1013193X-RAY DIFFRACTION99.85
4.567-5.2660.1621420.112794X-RAY DIFFRACTION99.323
5.266-6.430.1681150.1382376X-RAY DIFFRACTION98.888
6.43-9.0120.204840.1421878X-RAY DIFFRACTION99.594
9.012-47.7850.175440.1861100X-RAY DIFFRACTION97.466

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