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- PDB-8rtq: Bilirubin oxidase from Myrothecium verrucaria with G395T mutation -

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Basic information

Entry
Database: PDB / ID: 8rtq
TitleBilirubin oxidase from Myrothecium verrucaria with G395T mutation
ComponentsBilirubin oxidase
KeywordsOXIDOREDUCTASE / Trp-His covalent 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 / OXYGEN MOLECULE / SUCCINIC ACID / Bilirubin oxidase
Similarity search - Component
Biological speciesAlbifimbria verrucaria (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)124,66736
Polymers120,1392
Non-polymers4,52834
Water20,5191139
1
AAA: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,43617
Polymers60,0701
Non-polymers2,36616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,23119
Polymers60,0701
Non-polymers2,16218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.215, 200.681, 216.615
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: 60069.742 Da / Num. of mol.: 2 / Mutation: G395T
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 , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-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
#4: 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.: 1
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

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Non-polymers , 6 types, 1169 molecules

#5: 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
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE


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


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O4
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1139 / 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: 60.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 20% (w/v) PEG 3350, 0.1 M succinic acid pH 3.5, 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: 2.1→47.66 Å / Num. obs: 81954 / % possible obs: 95.6 % / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.11 / Rrim(I) all: 0.222 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4596 / CC1/2: 0.586 / Rpim(I) all: 0.496 / Rrim(I) all: 0.996 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.66 Å / Cor.coef. Fo:Fc: 0.964 / SU B: 3.905 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.162
Details: Hydrogens have been added in their riding positions. The last refinement cycle was performed against all measured reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4026 4.9 %RANDOM SELECTION
Rwork0.153 81954 --
all0.154 ---
obs0.154 81954 95.333 %-
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: 21.047 Å2
Baniso -1Baniso -2Baniso -3
1-0.112 Å2-0 Å20 Å2
2---0.582 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8494 0 269 1139 9902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139207
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158234
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.67812630
X-RAY DIFFRACTIONr_angle_other_deg1.3161.59319001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80251123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11722.106527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02151317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0931563
X-RAY DIFFRACTIONr_chiral_restr0.0730.21203
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210610
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022230
X-RAY DIFFRACTIONr_nbd_refined0.2010.21693
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.28063
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24367
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24097
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2859
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.130.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.231
X-RAY DIFFRACTIONr_nbd_other0.1810.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.222
X-RAY DIFFRACTIONr_mcbond_it1.422.0234326
X-RAY DIFFRACTIONr_mcbond_other1.4172.0224325
X-RAY DIFFRACTIONr_mcangle_it2.1593.035419
X-RAY DIFFRACTIONr_mcangle_other2.1593.0315420
X-RAY DIFFRACTIONr_scbond_it2.2052.3164879
X-RAY DIFFRACTIONr_scbond_other2.2052.3164880
X-RAY DIFFRACTIONr_scangle_it3.4653.3977180
X-RAY DIFFRACTIONr_scangle_other3.4643.3977181
X-RAY DIFFRACTIONr_lrange_it4.97324.93510429
X-RAY DIFFRACTIONr_lrange_other4.72424.36610153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.2693090.2415827X-RAY DIFFRACTION97.428
2.154-2.2130.2672740.2365690X-RAY DIFFRACTION97.007
2.213-2.2770.2582820.2195456X-RAY DIFFRACTION96.082
2.277-2.3470.2272560.2015341X-RAY DIFFRACTION96.734
2.347-2.4240.2662870.1915185X-RAY DIFFRACTION96.542
2.424-2.5090.2532670.1894973X-RAY DIFFRACTION96.377
2.509-2.6030.2482160.1754829X-RAY DIFFRACTION96.15
2.603-2.7090.2262380.1584635X-RAY DIFFRACTION95.869
2.709-2.830.1992580.1514357X-RAY DIFFRACTION94.589
2.83-2.9670.1972230.1354226X-RAY DIFFRACTION95.575
2.967-3.1270.1852340.1223992X-RAY DIFFRACTION95.46
3.127-3.3160.1651870.1213782X-RAY DIFFRACTION95.02
3.316-3.5440.1471630.123599X-RAY DIFFRACTION94.904
3.544-3.8260.171690.1243276X-RAY DIFFRACTION93.386
3.826-4.1890.1391720.113044X-RAY DIFFRACTION94.008
4.189-4.6790.1331470.0992749X-RAY DIFFRACTION93.722
4.679-5.3950.1461090.112395X-RAY DIFFRACTION91.722
5.395-6.5890.1821050.1572046X-RAY DIFFRACTION91.962
6.589-9.2380.174810.161603X-RAY DIFFRACTION90.635
9.238-47.660.306490.207924X-RAY DIFFRACTION89.43

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