[English] 日本語
Yorodumi
- PDB-6h3o: Alcohol oxidase from Phanerochaete chrysosporium mutant F101S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h3o
TitleAlcohol oxidase from Phanerochaete chrysosporium mutant F101S
ComponentsAlcohol oxidase
KeywordsOXIDOREDUCTASE / alcohol oxidase / octamer / FAD-binding domain / mutant F101S
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 1. / 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
FLAVIN-ADENINE DINUCLEOTIDE / Alcohol oxidase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNguyen, Q.-T. / Romero, E. / Dijkman, W.P. / de Vasconcellos, S.P. / Binda, C. / Mattevi, A. / Fraaije, M.W.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Union635734 Italy
CitationJournal: Biochemistry / Year: 2018
Title: Structure-Based Engineering of Phanerochaete chrysosporium Alcohol Oxidase for Enhanced Oxidative Power toward Glycerol.
Authors: Nguyen, Q.T. / Romero, E. / Dijkman, W.P. / de Vasconcellos, S.P. / Binda, C. / Mattevi, A. / Fraaije, M.W.
History
DepositionJul 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 17, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alcohol oxidase
B: Alcohol oxidase
C: Alcohol oxidase
D: Alcohol oxidase
E: Alcohol oxidase
F: Alcohol oxidase
G: Alcohol oxidase
H: Alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)587,05118
Polymers580,5828
Non-polymers6,46910
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area64820 Å2
ΔGint-246 kcal/mol
Surface area151960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.074, 203.553, 116.009
Angle α, β, γ (deg.)90.00, 104.64, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Alcohol oxidase


Mass: 72572.805 Da / Num. of mol.: 8 / Mutation: F101S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Gene: aox1 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / References: UniProt: T2M2J4
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 14% (w/v) PEG3350 and 0.2 M potassium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9726 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9726 Å / Relative weight: 1
ReflectionResolution: 2.5→49.2 Å / Num. obs: 170450 / % possible obs: 98.5 % / Redundancy: 2.9 % / CC1/2: 0.979 / Net I/σ(I): 6.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8298 / CC1/2: 0.485 / Rpim(I) all: 0.65 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H3G

6h3g


Resolution: 2.5→49.19 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.858 / SU B: 17.355 / SU ML: 0.354 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 8397 4.9 %RANDOM
Rwork0.21015 ---
obs0.21387 162012 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.869 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å20.87 Å2
2--1.78 Å2-0 Å2
3----2.12 Å2
Refinement stepCycle: 1 / Resolution: 2.5→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40647 0 436 695 41778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01442124
X-RAY DIFFRACTIONr_bond_other_d0.0010.01736806
X-RAY DIFFRACTIONr_angle_refined_deg1.221.67757262
X-RAY DIFFRACTIONr_angle_other_deg0.7961.64586569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80955181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31521.8742273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.609156857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.73415311
X-RAY DIFFRACTIONr_chiral_restr0.0560.25422
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0247665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027591
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_it1.4383.34620745
X-RAY DIFFRACTIONr_mcbond_other1.4373.34620744
X-RAY DIFFRACTIONr_mcangle_it2.3455.01625919
X-RAY DIFFRACTIONr_mcangle_other2.3455.01625920
X-RAY DIFFRACTIONr_scbond_it1.4233.47221379
X-RAY DIFFRACTIONr_scbond_other1.4233.47221379
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3685.14731344
X-RAY DIFFRACTIONr_long_range_B_refined4.0853948366
X-RAY DIFFRACTIONr_long_range_B_other4.08239.00548342
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 600 -
Rwork0.337 11728 -
obs--96.83 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more