[English] 日本語
Yorodumi
- PDB-6i22: Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i22
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 / Aureochrome1-like protein
Similarity search - Component
Biological speciesOchromonas danica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 1.2Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aureochrome1-like protein
B: Aureochrome1-like protein
C: Aureochrome1-like protein
D: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3608
Polymers59,5354
Non-polymers1,8254
Water9,548530
1
A: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3402
Polymers14,8841
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3402
Polymers14,8841
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3402
Polymers14,8841
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3402
Polymers14,8841
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.180, 91.510, 99.840
Angle α, β, γ (deg.)90.00, 131.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-536-

HOH

21D-501-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLUGLUAA179 - 3112 - 134
21ALAALAGLUGLUBB179 - 3112 - 134
12ALAALAASNASNAA179 - 3102 - 133
22ALAALAASNASNCC179 - 3102 - 133
13ALAALAASNASNAA179 - 3102 - 133
23ALAALAASNASNDD179 - 3102 - 133
14ALAALAASNASNBB179 - 3102 - 133
24ALAALAASNASNCC179 - 3102 - 133
15ALAALAASNASNBB179 - 3102 - 133
25ALAALAASNASNDD179 - 3102 - 133
16GLYGLYGLUGLUCC178 - 3111 - 134
26GLYGLYGLUGLUDD178 - 3111 - 134

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Aureochrome1-like protein


Mass: 14883.666 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 1.5-3 M Na malonate, 0.1 M Tris.acetate / PH range: 7.5 - 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.66→71.05 Å / Num. obs: 117045 / % possible obs: 98 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.089 / Net I/σ(I): 12
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 8720 / CC1/2: 0.543 / Rrim(I) all: 1.201 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A8B

5a8b


Resolution: 1.66→71.05 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.528 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 5747 4.9 %RANDOM
Rwork0.20303 ---
obs0.20389 111245 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.452 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å2-0.03 Å2
2--1.49 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.66→71.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4180 0 124 530 4834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134467
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174043
X-RAY DIFFRACTIONr_angle_refined_deg1.661.696091
X-RAY DIFFRACTIONr_angle_other_deg1.4211.6019413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81423.554242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25715743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4341526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02909
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_it1.4312.3772170
X-RAY DIFFRACTIONr_mcbond_other1.4312.3742169
X-RAY DIFFRACTIONr_mcangle_it2.2933.5442717
X-RAY DIFFRACTIONr_mcangle_other2.2933.5472718
X-RAY DIFFRACTIONr_scbond_it2.1012.7362297
X-RAY DIFFRACTIONr_scbond_other2.1012.7362296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3273.9723366
X-RAY DIFFRACTIONr_long_range_B_refined6.90229.7015560
X-RAY DIFFRACTIONr_long_range_B_other6.90229.6995561
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A41910.1
12B41910.1
21A38610.14
22C38610.14
31A38640.14
32D38640.14
41B38820.13
42C38820.13
51B38800.13
52D38800.13
61C42640.08
62D42640.08
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 453 -
Rwork0.354 8264 -
obs--99.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.55471.10470.41862.55860.09433.7380.05160.1094-0.2924-0.05640-0.04660.3878-0.1004-0.05160.0471-0.0241-0.00790.0645-0.01810.036832.3523-1.977725.5966
23.72350.4030.23682.89130.9642.5555-0.0617-0.08720.4853-0.0559-0.0358-0.0368-0.26950.13020.09740.0313-0.0237-0.01510.0671-0.01660.072912.95551.25488.2688
31.98640.581-0.03282.22580.15163.53770.03880.14790.2277-0.0952-0.03260.0896-0.4211-0.0138-0.00630.05960.0050.00820.03070.01890.031745.290626.968323.7074
43.6464-0.1147-0.19192.0369-0.67272.0238-0.0248-0.0034-0.4249-0.0906-0.02960.07750.2229-0.13730.05440.0403-0.01870.01290.0295-0.00370.057161.89418.06554.9145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A179 - 311
2X-RAY DIFFRACTION2B178 - 311
3X-RAY DIFFRACTION3C178 - 311
4X-RAY DIFFRACTION4D179 - 311

+
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