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- PDB-6i3l: Bilirubin oxidase from Myrothecium verrucaria, mutant W396F -

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Basic information

Entry
Database: PDB / ID: 6i3l
TitleBilirubin oxidase from Myrothecium verrucaria, mutant W396F
ComponentsBilirubin oxidase
KeywordsOXIDOREDUCTASE / enzymatic activity / mutant
Function / homology
Function and homology information


bilirubin oxidase activity / bilirubin oxidase / copper ion binding
Similarity search - Function
Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / OXYGEN MOLECULE / SUCCINIC ACID / Bilirubin oxidase
Similarity search - Component
Biological speciesAlbifimbria verrucaria (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoval, T. / Svecova, L. / Skalova, T. / Kolenko, P. / Duskova, J. / Ostergaard, L.H. / Dohnalek, J.
Funding support Czech Republic, 5items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLM2015043 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0109 Czech Republic
Czech Academy of Sciences86652036 Czech Republic
CitationJournal: Sci Rep / Year: 2019
Title: Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer.
Authors: Koval, T. / Svecova, L. / Ostergaard, L.H. / Skalova, T. / Duskova, J. / Hasek, J. / Kolenko, P. / Fejfarova, K. / Stransky, J. / Trundova, M. / Dohnalek, J.
History
DepositionNov 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bilirubin oxidase
B: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,86030
Polymers119,9412
Non-polymers3,91828
Water22,7531263
1
A: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,96415
Polymers59,9711
Non-polymers1,99414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,89515
Polymers59,9711
Non-polymers1,92514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.250, 200.663, 217.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bilirubin oxidase /


Mass: 59970.648 Da / Num. of mol.: 2 / Mutation: W396F
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-Glycam 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
[]{[(4+1)][b-D-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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 1287 molecules

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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#5: Chemical
ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1263 / 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: 3.1 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 3.1
Details: 14% (w/v) PEG 3350, 0.1 M succinic acid, protein concentration 25 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2 70 kV / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jul 17, 2018 / Details: HELIOS optics for MetalJet
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 2.1→45.54 Å / Num. obs: 83782 / % possible obs: 97.3 % / Observed criterion σ(I): -3.7 / Redundancy: 4.8 % / Biso Wilson estimate: 16.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.095 / Rrim(I) all: 0.212 / Net I/σ(I): 7.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3866 / CC1/2: 0.697 / Rpim(I) all: 0.386 / Rrim(I) all: 0.759 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1200011284

Resolution: 2.1→45.54 Å / Cor.coef. Fo:Fc: 0.961 / SU B: 3.772 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.165
Stereochemistry target values: STEREOCHEMISTRY LIBRARY OF CCP4 v. 7.0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19594 4179 5 %Random selection
Rwork0.15945 ---
obs0.16064 83773 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.839 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.17 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.1→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8480 0 233 1263 9976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139185
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178028
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.67512598
X-RAY DIFFRACTIONr_angle_other_deg1.2991.58618680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.63551132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35221.981525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.379151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.171563
X-RAY DIFFRACTIONr_chiral_restr0.0690.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022054
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_it1.2891.9184335
X-RAY DIFFRACTIONr_mcbond_other1.2831.9184334
X-RAY DIFFRACTIONr_mcangle_it1.972.8735432
X-RAY DIFFRACTIONr_mcangle_other1.972.8745433
X-RAY DIFFRACTIONr_scbond_it2.0072.1714849
X-RAY DIFFRACTIONr_scbond_other2.0072.1714850
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1683.1847133
X-RAY DIFFRACTIONr_long_range_B_refined4.97823.76410448
X-RAY DIFFRACTIONr_long_range_B_other4.62123.02210135
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å
RfactorNum. reflection% reflection
Rfree0.277 292 -
Rwork0.225 4922 -
obs--82.83 %

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