[English] 日本語
Yorodumi
- PDB-8q5f: Crystal structure of miniSOG protein from Arabidopsis thaliana wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q5f
TitleCrystal structure of miniSOG protein from Arabidopsis thaliana with covalent FMN
ComponentsminiSOG
KeywordsSIGNALING PROTEIN / covalent flavinylation
Function / homologyFLAVIN MONONUCLEOTIDE
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Fixing Flavins: Hijacking a Flavin Transferase for Equipping Flavoproteins with a Covalent Flavin Cofactor.
Authors: Tong, Y. / Kaya, S.G. / Russo, S. / Rozeboom, H.J. / Wijma, H.J. / Fraaije, M.W.
History
DepositionAug 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 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: miniSOG
B: miniSOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2504
Polymers26,3382
Non-polymers9132
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-11 kcal/mol
Surface area12080 Å2
Unit cell
Length a, b, c (Å)62.821, 130.314, 67.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1144-

HOH

21B-1138-

HOH

-
Components

#1: Protein miniSOG


Mass: 13168.835 Da / Num. of mol.: 2 / Mutation: A51D T52I V53V Q54A K55G I56A R57T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 19% polyacrylic acid 5100, 100 mM Hepes ppH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96456 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96456 Å / Relative weight: 1
ReflectionResolution: 2→67.43 Å / Num. obs: 17411 / % possible obs: 91.8 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.036 / Rrim(I) all: 0.078 / Χ2: 1.04 / Net I/σ(I): 11.9 / Num. measured all: 69790
Reflection shellResolution: 2→2.05 Å / % possible obs: 98.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.98 / Num. measured all: 5601 / Num. unique obs: 1375 / CC1/2: 0.697 / Rpim(I) all: 0.514 / Rrim(I) all: 1.114 / Χ2: 1.01 / Net I/σ(I) obs: 1.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→56.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.961 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22839 866 5 %RANDOM
Rwork0.18827 ---
obs0.19035 16522 90.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.602 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å2-0 Å2
2--0.04 Å20 Å2
3----2.58 Å2
Refinement stepCycle: 1 / Resolution: 2→56.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 60 84 1914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121872
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161743
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.652534
X-RAY DIFFRACTIONr_angle_other_deg0.4711.574015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.769514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57910320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
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_it3.5483.752870
X-RAY DIFFRACTIONr_mcbond_other3.5423.753870
X-RAY DIFFRACTIONr_mcangle_it4.6076.7041084
X-RAY DIFFRACTIONr_mcangle_other4.626.7081085
X-RAY DIFFRACTIONr_scbond_it4.9734.3571002
X-RAY DIFFRACTIONr_scbond_other4.9424.3551000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5467.7051451
X-RAY DIFFRACTIONr_long_range_B_refined9.00743.232198
X-RAY DIFFRACTIONr_long_range_B_other8.99943.12183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 58 -
Rwork0.301 1313 -
obs--97.79 %

+
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