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- PDB-8rto: Bilirubin oxidase from Myrothecium verrucaria in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 8rto
TitleBilirubin oxidase from Myrothecium verrucaria in complex with ATP
ComponentsBilirubin oxidase
KeywordsOXIDOREDUCTASE / Trp-His covalent link / complex / ATP
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
ADENOSINE-5'-TRIPHOSPHATE / COPPER (II) ION / OXYGEN MOLECULE / Bilirubin oxidase
Similarity search - Component
Biological speciesAlbifimbria verrucaria (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
CCC: Bilirubin oxidase
DDD: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,07440
Polymers240,0394
Non-polymers7,03536
Water26,3921465
1
AAA: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,88511
Polymers60,0101
Non-polymers1,87510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8149
Polymers60,0101
Non-polymers1,8048
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,72311
Polymers60,0101
Non-polymers1,71310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6529
Polymers60,0101
Non-polymers1,6428
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.468, 204.726, 221.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Bilirubin oxidase


Mass: 60009.688 Da / Num. of mol.: 4
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, 8 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.: 6
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 , 5 types, 1493 molecules

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


Mass: 63.546 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#7: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1465 / 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: 61.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 14% (w/v) PEG 3350, 0.1 M citric acid, pH 3.5; 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.4→46.95 Å / Num. obs: 106801 / % possible obs: 90.4 % / Observed criterion σ(I): -3.7 / Redundancy: 4.2 % / Biso Wilson estimate: 23.6 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.065 / Rrim(I) all: 0.139 / Net I/σ(I): 10.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5409 / CC1/2: 0.689 / Rpim(I) all: 0.346 / Rrim(I) all: 0.73 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.499 Å / Cor.coef. Fo:Fc: 0.949 / SU B: 5.838 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.329
Details: Hydrogens have been added in their riding positions. The last refinement cycle was performed against all measured reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.22425 5384 5 %RANDOM SELECTION
Rwork0.1701 106800 --
all0.17 ---
obs0.16969 106800 89.841 %-
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: 28.048 Å2
Baniso -1Baniso -2Baniso -3
1-0.513 Å20 Å2-0 Å2
2---0.883 Å2-0 Å2
3---0.369 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16962 0 398 1465 18825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01317992
X-RAY DIFFRACTIONr_bond_other_d0.0010.01515918
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.67824696
X-RAY DIFFRACTIONr_angle_other_deg1.2521.5936665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.38452143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10722.1191005
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.903152542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.77215116
X-RAY DIFFRACTIONr_chiral_restr0.0720.22359
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0220599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024341
X-RAY DIFFRACTIONr_nbd_refined0.1970.23539
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.215966
X-RAY DIFFRACTIONr_nbtor_refined0.1720.28365
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.28046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.21263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.211
X-RAY DIFFRACTIONr_metal_ion_refined0.1440.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.240
X-RAY DIFFRACTIONr_nbd_other0.2370.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.215
X-RAY DIFFRACTIONr_mcbond_it2.3412.8488546
X-RAY DIFFRACTIONr_mcbond_other2.342.8488545
X-RAY DIFFRACTIONr_mcangle_it3.5914.26310680
X-RAY DIFFRACTIONr_mcangle_other3.5914.26410681
X-RAY DIFFRACTIONr_scbond_it2.6783.1579444
X-RAY DIFFRACTIONr_scbond_other2.6783.1579444
X-RAY DIFFRACTIONr_scangle_it4.2224.66714009
X-RAY DIFFRACTIONr_scangle_other4.2224.66814010
X-RAY DIFFRACTIONr_lrange_it6.12333.3920020
X-RAY DIFFRACTIONr_lrange_other6.09333.32319786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)Rfactor Rfree error
2.4-2.4620.3293940.261767193.16
2.462-2.5290.2963680.236753393.17
2.529-2.6030.2733870.221727592.64
2.603-2.6820.2993980.214697792.38
2.682-2.770.2793470.196683492.02
2.77-2.8670.2673340.187656591.63
2.867-2.9750.2253760.16628491.33
2.975-3.0960.2243250.169598390.78
3.096-3.2330.2522950.172582990.39
3.233-3.390.2273230.173541389.46
3.39-3.5720.2072680.165521389.38
3.572-3.7870.2062420.16490688.61
3.787-4.0470.1780.132453787.38255
4.047-4.3680.1862140.126422186.59
4.368-4.7810.1682020.136385186.27
4.781-5.3390.1832000.137346885.54
5.339-6.1510.2011690.135306784.67
6.151-7.5020.2061210.171260884.25
7.502-10.4760.151130.13199782.52
10.476-46.4990.205530.222118579.87

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