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- PDB-6i3k: Bilirubin oxidase from Myrothecium verrucaria, mutant W396A in co... -

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Basic information

Entry
Database: PDB / ID: 6i3k
TitleBilirubin oxidase from Myrothecium verrucaria, mutant W396A in complex with ferricyanide
ComponentsBilirubin oxidase
KeywordsOXIDOREDUCTASE / enzymatic activity / mutant / complex
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 / HEXACYANOFERRATE(3-) / : / DI(HYDROXYETHYL)ETHER / SUCCINIC ACID / Bilirubin oxidase
Similarity search - Component
Biological speciesAlbifimbria verrucaria (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / 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_alt_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_alt_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_label_asym_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_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr2_label_seq_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)125,32140
Polymers119,7892
Non-polymers5,53238
Water30,0851670
1
A: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,82121
Polymers59,8951
Non-polymers2,92620
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,50019
Polymers59,8951
Non-polymers2,60618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.906, 201.803, 217.869
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
11A-1407-

HOH

21B-1312-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bilirubin oxidase /


Mass: 59894.555 Da / Num. of mol.: 2 / Mutation: W396A
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.: 3
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.: 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 , 8 types, 1704 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-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6FeN6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H6O4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#9: 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
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1670 / 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: 3.2 Å3/Da / Density % sol: 61 %
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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→47.93 Å / Num. obs: 195423 / % possible obs: 99.6 % / Observed criterion σ(I): -3.7 / Redundancy: 3.8 % / Biso Wilson estimate: 10.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.044 / Rrim(I) all: 0.086 / Net I/σ(I): 9.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 9686 / CC1/2: 0.7 / Rpim(I) all: 0.373 / Rrim(I) all: 0.738 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1200011284

Resolution: 1.6→47.93 Å / Cor.coef. Fo:Fc: 0.978 / SU B: 1.203 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.057
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
Rfree0.15402 9580 4.9 %Random selection
Rwork0.13122 ---
obs0.13189 195423 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.546 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0 Å2
2---0.09 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.6→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8468 0 333 1670 10471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0139653
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178435
X-RAY DIFFRACTIONr_angle_refined_deg1.671.66813309
X-RAY DIFFRACTIONr_angle_other_deg1.4561.58819707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25451224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01422.176547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.367151414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6151566
X-RAY DIFFRACTIONr_chiral_restr0.0890.21259
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211033
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022113
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_it1.081.3864505
X-RAY DIFFRACTIONr_mcbond_other1.0791.3864504
X-RAY DIFFRACTIONr_mcangle_it1.5552.0785691
X-RAY DIFFRACTIONr_mcangle_other1.5552.0795692
X-RAY DIFFRACTIONr_scbond_it1.8861.6365146
X-RAY DIFFRACTIONr_scbond_other1.8861.6375147
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8352.3927560
X-RAY DIFFRACTIONr_long_range_B_refined5.35718.71710810
X-RAY DIFFRACTIONr_long_range_B_other4.46717.16310278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å
RfactorNum. reflection% reflection
Rfree0.254 679 4.7 %
Rwork0.248 13704 -
obs--99.75 %

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