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- PDB-6iqy: High resolution structure of bilirubin oxidase from Myrothecium v... -

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Basic information

Entry
Database: PDB / ID: 6iqy
TitleHigh resolution structure of bilirubin oxidase from Myrothecium verrucaria - M467Q mutant, anaerobically prepared
ComponentsBilirubin oxidase
KeywordsOXIDOREDUCTASE / Multicopper oxydase
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
ACETATE ION / COPPER (II) ION / Bilirubin oxidase
Similarity search - Component
Biological speciesMyrothecium verrucaria (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShibata, N. / Akter, M. / Higuchi, Y.
CitationJournal: Chemistry / Year: 2018
Title: Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase.
Authors: Akter, M. / Tokiwa, T. / Shoji, M. / Nishikawa, K. / Shigeta, Y. / Sakurai, T. / Higuchi, Y. / Kataoka, K. / Shibata, N.
History
DepositionNov 9, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 21, 2018ID: 5ZD7
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
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.occupancy / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 2.1Nov 22, 2023Group: 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)124,05725
Polymers121,0902
Non-polymers2,96723
Water26,6801481
1
A: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,98312
Polymers60,5451
Non-polymers1,43711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,07513
Polymers60,5451
Non-polymers1,52912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.298, 152.253, 69.908
Angle α, β, γ (deg.)90.00, 91.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bilirubin oxidase /


Mass: 60545.227 Da / Num. of mol.: 2 / Mutation: M467Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myrothecium verrucaria (fungus) / Plasmid: pPICBO / Production host: Komagataella pastoris (fungus) / References: UniProt: Q12737, bilirubin oxidase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1500 molecules

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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1481 / 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: 2.61 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES PH 5.5, 12% (W/V) PEG 8000, 0.1M CALCIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 162206 / % possible obs: 99.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 11.49
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.22 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XLL

2xll


Resolution: 1.6→45.861 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.08
RfactorNum. reflection% reflection
Rfree0.2248 1995 1.23 %
Rwork0.1912 --
obs0.1916 162075 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→45.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8526 0 166 1481 10173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089094
X-RAY DIFFRACTIONf_angle_d1.1912464
X-RAY DIFFRACTIONf_dihedral_angle_d13.593299
X-RAY DIFFRACTIONf_chiral_restr0.0551346
X-RAY DIFFRACTIONf_plane_restr0.0071644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5991-1.63910.30931470.262711266X-RAY DIFFRACTION98
1.6391-1.68340.2971360.231911367X-RAY DIFFRACTION100
1.6834-1.73290.2471430.216411435X-RAY DIFFRACTION100
1.7329-1.78890.24971380.204111529X-RAY DIFFRACTION100
1.7889-1.85280.25721510.199311412X-RAY DIFFRACTION100
1.8528-1.9270.25991370.237311411X-RAY DIFFRACTION99
1.927-2.01470.25071490.198311412X-RAY DIFFRACTION100
2.0147-2.12090.19841420.194711434X-RAY DIFFRACTION99
2.1209-2.25380.23971470.205311367X-RAY DIFFRACTION99
2.2538-2.42780.25711410.186411477X-RAY DIFFRACTION100
2.4278-2.67210.21431460.189411469X-RAY DIFFRACTION100
2.6721-3.05870.19761400.180511447X-RAY DIFFRACTION100
3.0587-3.85330.19181410.170811480X-RAY DIFFRACTION100
3.8533-45.87940.20291370.165411574X-RAY DIFFRACTION100

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