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- PDB-6o9n: Structural insights on a new fungal aryl-alcohol oxidase -

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Basic information

Entry
Database: PDB / ID: 6o9n
TitleStructural insights on a new fungal aryl-alcohol oxidase
ComponentsAryl-alcohol oxidase
KeywordsOXIDOREDUCTASE / aryl-alcohol oxidase AA3 family Myceliophthora thermophila
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / FLAVIN-ADENINE DINUCLEOTIDE / GMC oxidoreductase-like protein
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsKadowaki, M.A.S. / Polikarpov, I.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Enzymatic versatility and thermostability of a new aryl-alcohol oxidase from Thermothelomyces thermophilus M77.
Authors: Kadowaki, M.A.S. / Higasi, P.M.R. / de Godoy, M.O. / de Araujo, E.A. / Godoy, A.S. / Prade, R.A. / Polikarpov, I.
History
DepositionMar 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Sep 30, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_abbrev ..._chem_comp.pdbx_synonyms / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Aryl-alcohol oxidase
B: Aryl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,39218
Polymers138,3732
Non-polymers5,02016
Water9,242513
1
A: Aryl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,90610
Polymers69,1861
Non-polymers2,7199
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aryl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4878
Polymers69,1861
Non-polymers2,3007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.854, 109.696, 220.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aryl-alcohol oxidase / / GMC oxidoreductase-like protein


Mass: 69186.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (fungus) / Strain: M77 / Gene: MYCTH_2299749 / Plasmid: pEXPYR / Production host: Aspergillus nidulans FGSC A4 (mold) / Strain (production host): A773 / References: UniProt: G2PZJ2, aryl-alcohol oxidase

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Sugars , 3 types, 7 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.: 1 / Source method: isolated from a natural 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.: 3 / Source method: isolated from a natural 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
#5: 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.: 3 / Source method: isolated from a natural 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 , 7 types, 522 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#8: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C11H26N2O6 / Comment: pH buffer*YM
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#10: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Tris-HCl, pH 9.0, 15% w/v PEG6000, 0.2 M calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 27, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.598→98.192 Å / Num. obs: 48645 / % possible obs: 99.7 % / Redundancy: 8.1 % / Net I/σ(I): 7.3
Reflection shellResolution: 2.6→2.68 Å / Num. unique obs: 4296

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FIM

3fim


Resolution: 2.598→98.192 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 23.89 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2506 2457 5.05 %
Rwork0.1936 --
obs0.1965 48645 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.598→98.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9266 0 328 513 10107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119928
X-RAY DIFFRACTIONf_angle_d1.25713663
X-RAY DIFFRACTIONf_dihedral_angle_d5.2687740
X-RAY DIFFRACTIONf_chiral_restr0.0641528
X-RAY DIFFRACTIONf_plane_restr0.0081771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.598-2.6480.32271420.2612533X-RAY DIFFRACTION100
2.648-2.7020.33631400.24582509X-RAY DIFFRACTION100
2.702-2.76080.30821340.24092535X-RAY DIFFRACTION100
2.7608-2.8250.29021270.24352519X-RAY DIFFRACTION100
2.825-2.89570.31361250.23532575X-RAY DIFFRACTION100
2.8957-2.9740.31711190.23412516X-RAY DIFFRACTION100
2.974-3.06150.28231560.21912536X-RAY DIFFRACTION100
3.0615-3.16030.27831220.21832530X-RAY DIFFRACTION100
3.1603-3.27330.27011420.22452536X-RAY DIFFRACTION100
3.2733-3.40430.26621350.21552540X-RAY DIFFRACTION100
3.4043-3.55930.27421320.20712586X-RAY DIFFRACTION100
3.5593-3.74690.25481580.18562543X-RAY DIFFRACTION100
3.7469-3.98170.25261400.17512554X-RAY DIFFRACTION100
3.9817-4.28910.18691320.14892573X-RAY DIFFRACTION100
4.2891-4.72080.21751280.13552591X-RAY DIFFRACTION100
4.7208-5.40380.17811330.15332617X-RAY DIFFRACTION100
5.4038-6.8080.20871360.17242636X-RAY DIFFRACTION100
6.808-98.26230.21821560.1872759X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -42.8693 Å / Origin y: 28.5274 Å / Origin z: 274.1289 Å
111213212223313233
T0.1983 Å2-0.0112 Å20.0029 Å2-0.226 Å20.0063 Å2--0.2528 Å2
L0.1299 °2-0.0762 °2-0.2655 °2-0.0755 °20.2271 °2--0.8559 °2
S0.025 Å °0.0085 Å °0.0245 Å °-0.0183 Å °0.0107 Å °-0.0153 Å °-0.0463 Å °-0.025 Å °-0.0363 Å °
Refinement TLS groupSelection details: all

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