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- PDB-8rtp: Bilirubin oxidase from Myrothecium verrucaria in complex with NAD+ -

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Basic information

Entry
Database: PDB / ID: 8rtp
TitleBilirubin oxidase from Myrothecium verrucaria in complex with NAD+
ComponentsBilirubin oxidase
KeywordsOXIDOREDUCTASE / Trp-His cross link / complex / NAD+
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXYGEN MOLECULE / R-1,2-PROPANEDIOL / 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)124,85125
Polymers120,0192
Non-polymers4,83223
Water18,2491013
1
AAA: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,63913
Polymers60,0101
Non-polymers2,62912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,21312
Polymers60,0101
Non-polymers2,20311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.727, 202.441, 224.762
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11BBB-607-

PG4

21BBB-1169-

HOH

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Bilirubin oxidase


Mass: 60009.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Covalent link between side chains of Trp396 and His398.
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 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.: 3
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 , 8 types, 1032 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-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#9: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1013 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 3.1
Details: 14% (w/v) PEG 3350, 0.1 M succinic acid, pH 3.1, protein concentration 25 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 PILATUS 6M / Detector: PIXEL / Date: May 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→46.992 Å / Num. obs: 87859 / % possible obs: 98.9 % / Observed criterion σ(I): -3.7 / Redundancy: 5.4 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.055 / Rrim(I) all: 0.128 / Net I/σ(I): 10.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2 / Num. unique obs: 4073 / CC1/2: 0.723 / Rpim(I) all: 0.354 / Rrim(I) all: 0.782 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.992 Å / Cor.coef. Fo:Fc: 0.959 / SU B: 3.81 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.161
Details: Hydrogens have been added in their riding positions. The last refinement cycle was performed against all measured reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 4435 5 %RANDOM SELECTION
Rwork0.1692 87858 --
all0.169 ---
obs0.1686 87858 98.749 %-
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: 32.582 Å2
Baniso -1Baniso -2Baniso -3
1--1.683 Å20 Å20 Å2
2--0.052 Å20 Å2
3---1.631 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8476 0 295 1013 9784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139143
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158123
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.67912540
X-RAY DIFFRACTIONr_angle_other_deg1.2921.59218730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80451095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26622.016516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.513151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4351562
X-RAY DIFFRACTIONr_chiral_restr0.0730.21197
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022215
X-RAY DIFFRACTIONr_nbd_refined0.2010.21741
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.28050
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24289
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24028
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2885
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0790.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1710.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.221
X-RAY DIFFRACTIONr_nbd_other0.1980.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.219
X-RAY DIFFRACTIONr_mcbond_it2.5943.2654294
X-RAY DIFFRACTIONr_mcbond_other2.5893.2644293
X-RAY DIFFRACTIONr_mcangle_it3.534.8925373
X-RAY DIFFRACTIONr_mcangle_other3.5294.8935374
X-RAY DIFFRACTIONr_scbond_it3.1343.5924847
X-RAY DIFFRACTIONr_scbond_other3.1283.5894846
X-RAY DIFFRACTIONr_scangle_it4.5635.3247151
X-RAY DIFFRACTIONr_scangle_other4.5635.3247152
X-RAY DIFFRACTIONr_lrange_it6.16639.46810400
X-RAY DIFFRACTIONr_lrange_other6.03138.90410152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.2983010.2625684X-RAY DIFFRACTION91.752
2.154-2.2130.2693220.2335934X-RAY DIFFRACTION98.303
2.213-2.2770.283280.2175818X-RAY DIFFRACTION99.854
2.277-2.3470.2742750.25723X-RAY DIFFRACTION99.751
2.347-2.4240.2272750.1875541X-RAY DIFFRACTION99.777
2.424-2.5090.2382700.1825373X-RAY DIFFRACTION99.858
2.509-2.6030.2363040.185104X-RAY DIFFRACTION99.467
2.603-2.7090.2172780.174959X-RAY DIFFRACTION99.771
2.709-2.8290.2212590.1664765X-RAY DIFFRACTION99.821
2.829-2.9670.2352520.1594564X-RAY DIFFRACTION99.71
2.967-3.1270.2242260.1534338X-RAY DIFFRACTION99.477
3.127-3.3150.2172360.1694082X-RAY DIFFRACTION99.539
3.315-3.5430.2082020.173883X-RAY DIFFRACTION99.489
3.543-3.8250.1991690.1653609X-RAY DIFFRACTION99.108
3.825-4.1870.1541920.1323289X-RAY DIFFRACTION98.5
4.187-4.6770.1931470.1333007X-RAY DIFFRACTION98.748
4.677-5.3920.1751430.1462665X-RAY DIFFRACTION98.8732
5.392-6.5820.1991200.162262X-RAY DIFFRACTION98.43
6.582-9.2180.21880.1661780X-RAY DIFFRACTION98.212
9.218-46.9920.232480.2011043X-RAY DIFFRACTION95.7018

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