[English] 日本語
Yorodumi
- PDB-6i21: Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i21
TitleFlavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism
ComponentsAureochrome1-like protein
KeywordsTRANSCRIPTION / LOV Domain / FMN / Dark grown / fluorescence / light sensing / transcription factor PAS domain / Ochronomas danica
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Basic region leucine zipper / PAS-associated, C-terminal / PAC domain profile. / Basic-leucine zipper (bZIP) domain profile. / PAS domain / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) ...Basic region leucine zipper / PAS-associated, C-terminal / PAC domain profile. / Basic-leucine zipper (bZIP) domain profile. / PAS domain / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Aureochrome1-like protein
Similarity search - Component
Biological speciesOchromonas danica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRizkallah, P.J. / Kalvaitis, M.E. / Allemann, R.K. / Mart, R.J. / Johnson, L.A.
CitationJournal: Biochemistry / Year: 2019
Title: A Noncanonical Chromophore Reveals Structural Rearrangements of the Light-Oxygen-Voltage Domain upon Photoactivation.
Authors: Kalvaitis, M.E. / Johnson, L.A. / Mart, R.J. / Rizkallah, P. / Allemann, R.K.
History
DepositionOct 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,70015
Polymers15,0131
Non-polymers1,68814
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-17 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.389, 106.389, 67.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-408-

MG

21A-507-

HOH

31A-625-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Aureochrome1-like protein


Mass: 15012.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochromonas danica (eukaryote) / Gene: OdAUREO1 / Production host: Escherichia coli (E. coli) / References: UniProt: C5NSW6

-
Non-polymers , 6 types, 143 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10-25% PEG 2K or 3K, 100 mM Na Acetate or Na Citrate, pH 4.5 - 4.9 Protein conc 10 mg/ml

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→67.48 Å / Num. obs: 36515 / % possible obs: 100 % / Redundancy: 20.7 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.074 / Net I/av σ(I): 18.2 / Net I/σ(I): 18.2
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 21.3 % / Rmerge(I) obs: 2.595 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2637 / CC1/2: 0.644 / Rrim(I) all: 2.725 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A8B

5a8b


Resolution: 1.5→67.48 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.686 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.062 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20501 1886 5.2 %RANDOM
Rwork0.17304 ---
obs0.17476 34209 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.19 Å20 Å2
2---0.39 Å20 Å2
3---1.25 Å2
Refinement stepCycle: 1 / Resolution: 1.5→67.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 110 129 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021231
X-RAY DIFFRACTIONr_bond_other_d0.0020.021122
X-RAY DIFFRACTIONr_angle_refined_deg2.0062.0461668
X-RAY DIFFRACTIONr_angle_other_deg1.0443.0012612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59425.26357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79715195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.495157
X-RAY DIFFRACTIONr_chiral_restr0.1410.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021342
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02234
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_it1.8281.313564
X-RAY DIFFRACTIONr_mcbond_other1.8141.311563
X-RAY DIFFRACTIONr_mcangle_it2.3171.978712
X-RAY DIFFRACTIONr_mcangle_other2.3191.979713
X-RAY DIFFRACTIONr_scbond_it2.4371.71666
X-RAY DIFFRACTIONr_scbond_other2.4381.709665
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.72.424954
X-RAY DIFFRACTIONr_long_range_B_refined3.88417.8211582
X-RAY DIFFRACTIONr_long_range_B_other3.88317.8191583
X-RAY DIFFRACTIONr_rigid_bond_restr2.75432351
X-RAY DIFFRACTIONr_sphericity_free27.908580
X-RAY DIFFRACTIONr_sphericity_bonded8.61652385
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 128 -
Rwork0.313 2487 -
obs--99.32 %
Refinement TLS params.Method: refined / Origin x: 34.65 Å / Origin y: -34.5578 Å / Origin z: 7.8458 Å
111213212223313233
T0.0732 Å2-0.0364 Å2-0.0068 Å2-0.0914 Å20.0229 Å2--0.0116 Å2
L2.0908 °21.1951 °20.6484 °2-1.9877 °2-0.1778 °2--2.2232 °2
S-0.1129 Å °0.1876 Å °0.1398 Å °-0.216 Å °0.0839 Å °0.0441 Å °-0.0552 Å °-0.1509 Å °0.0291 Å °

+
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