[English] 日本語
Yorodumi
- PDB-8bjy: Engineered Fructosyl Peptide Oxidase - X02B mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bjy
TitleEngineered Fructosyl Peptide Oxidase - X02B mutant
ComponentsFructosyl Peptide Oxidase mutant (X02B)
KeywordsOXIDOREDUCTASE / FAD / deglycating enzyme / Amadori product / Fructosyl Peptide Oxidase
Function / homologysaccharopine oxidase activity / MTOX family / sarcosine oxidase activity / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily / flavin adenine dinucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / FAD dependent oxidoreductase domain-containing protein
Function and homology information
Biological speciesParastagonospora nodorum SN15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.475 Å
AuthorsEstiri, H. / Bhattacharya, S. / Rodriguez-Buitrago, J.A. / Parisini, E.
Funding support1items
OrganizationGrant numberCountry
Other governmentlzp-2020/2-0013
CitationJournal: Sci Rep / Year: 2023
Title: Tailoring FPOX enzymes for enhanced stability and expanded substrate recognition.
Authors: Estiri, H. / Bhattacharya, S. / Buitrago, J.A.R. / Castagna, R. / Legzdina, L. / Casucci, G. / Ricci, A. / Parisini, E. / Gautieri, A.
History
DepositionNov 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructosyl Peptide Oxidase mutant (X02B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1184
Polymers48,1491
Non-polymers9703
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-11 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.112, 88.493, 90.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Fructosyl Peptide Oxidase mutant (X02B)


Mass: 48148.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parastagonospora nodorum SN15 (fungus) / Strain: SN15 / ATCC MYA-4574 / FGSC 10173 / Gene: SNOG_08398 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0UIL6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 20000 16-26%, MES 0.1M pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.475→63.421 Å / Num. obs: 82805 / % possible obs: 96 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.07 / Net I/σ(I): 16.7
Reflection shellResolution: 1.475→1.501 Å / Redundancy: 11.3 % / Num. unique obs: 4255 / Rrim(I) all: 0.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata processing
Aimlessdata scaling
Cootmodel building
MOLREPphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y4J

6y4j


Resolution: 1.475→63.421 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.187 / SU B: 1.806 / SU ML: 0.061 / Average fsc free: 0.9493 / Average fsc work: 0.9548 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2149 4009 4.957 %
Rwork0.1893 76862 -
all0.191 --
obs-80871 93.716 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.915 Å2
Baniso -1Baniso -2Baniso -3
1-1.441 Å20 Å20 Å2
2---0.256 Å2-0 Å2
3----1.184 Å2
Refinement stepCycle: LAST / Resolution: 1.475→63.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 65 333 3740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123531
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163172
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.6494806
X-RAY DIFFRACTIONr_angle_other_deg0.5821.5737404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2635436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.113520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66910566
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.56610156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024004
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02719
X-RAY DIFFRACTIONr_nbd_refined0.2250.2666
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22936
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21654
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2247
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4490.213
X-RAY DIFFRACTIONr_nbd_other0.2890.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2570.218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0890.21
X-RAY DIFFRACTIONr_mcbond_it2.692.6891717
X-RAY DIFFRACTIONr_mcbond_other2.6892.6891717
X-RAY DIFFRACTIONr_mcangle_it3.8754.0252147
X-RAY DIFFRACTIONr_mcangle_other3.8784.0262148
X-RAY DIFFRACTIONr_scbond_it3.8013.1031814
X-RAY DIFFRACTIONr_scbond_other3.83.1061815
X-RAY DIFFRACTIONr_scangle_it5.5694.4662654
X-RAY DIFFRACTIONr_scangle_other5.5684.4682655
X-RAY DIFFRACTIONr_lrange_it7.98539.7364119
X-RAY DIFFRACTIONr_lrange_other7.88937.5384039
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.475-1.5140.3972040.37243120.37362870.8670.88171.83080.373
1.514-1.5550.4042710.3957310.3961650.8850.8997.3560.387
1.555-1.60.3612870.36856510.36859530.9140.9199.7480.358
1.6-1.6490.3572880.35555350.35558350.9150.91999.79430.335
1.649-1.7030.323040.31453400.31456500.9310.93999.89380.29
1.703-1.7630.282520.25851770.25954340.9520.95899.9080.231
1.763-1.830.2432410.21750170.21952580.9610.9691000.193
1.83-1.9040.2342900.18948160.19151060.9640.9771000.169
1.904-1.9890.2072540.16846210.1748780.9740.98299.93850.154
1.989-2.0860.2081650.1730920.17246890.9760.98369.46040.159
2.086-2.1980.2222170.18541370.18744320.9730.98298.24010.174
2.198-2.3320.1911720.17929580.1842420.9820.98473.78590.17
2.332-2.4920.1911960.17437660.17439620.9790.9851000.166
2.492-2.6920.2042060.16935070.17137130.9790.9851000.162
2.692-2.9480.221470.17133000.17334470.9760.9851000.168
2.948-3.2950.191300.16729820.16831120.9780.9841000.17
3.295-3.8030.1971190.16820000.1727640.9790.98376.66430.18
3.803-4.6540.1711070.14220980.14423660.9830.98893.19530.166
4.654-6.5640.223950.19817780.218730.9770.9861000.23
6.564-63.4210.191640.20210440.20211100.9830.97999.81980.248

+
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