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- PDB-6i3j: Bilirubin oxidase from Myrothecium verrucaria in complex with fer... -

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Basic information

Entry
Database: PDB / ID: 6i3j
TitleBilirubin oxidase from Myrothecium verrucaria in complex with ferricyanide
ComponentsBilirubin oxidase
KeywordsOXIDOREDUCTASE / Trp-His cross link / complex
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 / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / HEXACYANOFERRATE(3-) / R-1,2-PROPANEDIOL / SUCCINIC ACID / Bilirubin oxidase
Similarity search - Component
Biological speciesAlbifimbria verrucaria (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSvecova, L. / Koval, T. / 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 1.1Oct 30, 2019Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.2Apr 22, 2020Group: Data collection / Database references / Category: chem_comp / pdbx_related_exp_data_set / Item: _chem_comp.type
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 / pdbx_struct_special_symmetry / 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 / _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_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 / _pdbx_struct_special_symmetry.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 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)125,99238
Polymers120,0192
Non-polymers5,97236
Water9,854547
1
A: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,11420
Polymers60,0101
Non-polymers3,10419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,87818
Polymers60,0101
Non-polymers2,86817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.382, 203.846, 226.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11B-915-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bilirubin oxidase


Mass: 60009.688 Da / Num. of mol.: 2
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 , 4 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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-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
#4: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 1
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 , 7 types, 579 molecules

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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#7: Chemical
ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C6FeN6 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O4
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging 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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.59→47.3 Å / Num. obs: 48305 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 6.5 % / Biso Wilson estimate: 30.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.061 / Rrim(I) all: 0.157 / Net I/σ(I): 13.5
Reflection shellResolution: 2.59→2.67 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 2 / Num. unique obs: 4411 / CC1/2: 0.608 / Rpim(I) all: 0.428 / Rrim(I) all: 0.963 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XLL

2xll


Resolution: 2.59→47.3 Å / Cor.coef. Fo:Fc: 0.953 / SU B: 7.185 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.271
Stereochemistry target values: STEREOCHEMISTRY LIBRARY OF CCP4 v. 7.0, LIBRARY FOR FC6 ACCORDING TO CSD RELEASE 5.39
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 2442 5.1 %random selection
Rwork0.1601 ---
obs0.1618 48305 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0 Å2
2---1.72 Å20 Å2
3---2.19 Å2
Refinement stepCycle: 1 / Resolution: 2.59→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8476 0 357 547 9380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0149227
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177664
X-RAY DIFFRACTIONr_angle_refined_deg1.351.71612689
X-RAY DIFFRACTIONr_angle_other_deg0.8191.65818016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62751092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95421.915517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.747151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5541563
X-RAY DIFFRACTIONr_chiral_restr0.0590.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021780
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_it2.1623.6054328
X-RAY DIFFRACTIONr_mcbond_other2.1593.6044327
X-RAY DIFFRACTIONr_mcangle_it3.425.3995427
X-RAY DIFFRACTIONr_mcangle_other3.4215.4015428
X-RAY DIFFRACTIONr_scbond_it2.8084.0064898
X-RAY DIFFRACTIONr_scbond_other2.8084.0064898
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1945.9677260
X-RAY DIFFRACTIONr_long_range_B_refined6.01742.0169922
X-RAY DIFFRACTIONr_long_range_B_other6.00442.0129840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.657 Å
RfactorNum. reflection% reflection
Rfree0.327 173 -
Rwork0.271 3345 -
obs--99.86 %

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