[English] 日本語
Yorodumi
- PDB-5x4v: Roseoflavin substituted OaPAC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x4v
TitleRoseoflavin substituted OaPAC
ComponentsPhotoactivated adenylyl cyclase
KeywordsLYASE / cAMP / BLUF domain / optogenetics / photoactivation / allostery
Function / homology
Function and homology information


blue light photoreceptor activity / cAMP biosynthetic process / adenylate cyclase activity / FAD binding / cell projection / intracellular signal transduction / ATP binding / metal ion binding
Similarity search - Function
Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Acylphosphatase-like domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase
Similarity search - Domain/homology
Chem-RS3 / Family 3 adenylate cyclase
Similarity search - Component
Biological speciesCyanobacteria (blue-green algae)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsOhki, M. / Park, S.-Y.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular mechanism of photoactivation of a light-regulated adenylate cyclase.
Authors: Ohki, M. / Sato-Tomita, A. / Matsunaga, S. / Iseki, M. / Tame, J.R.H. / Shibayama, N. / Park, S.Y.
History
DepositionFeb 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photoactivated adenylyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4242
Polymers41,0191
Non-polymers4051
Water1,44180
1
A: Photoactivated adenylyl cyclase
hetero molecules

A: Photoactivated adenylyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8484
Polymers82,0382
Non-polymers8112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7130 Å2
ΔGint-68 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.872, 76.872, 204.785
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Photoactivated adenylyl cyclase


Mass: 41018.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobacteria (blue-green algae) / Production host: Cyanobacteria (blue-green algae) / References: UniProt: K9TLZ5*PLUS
#2: Chemical ChemComp-RS3 / 1-deoxy-1-[8-(dimethylamino)-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl]-D-ribitol / Roseoflavin


Mass: 405.405 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H23N5O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100mM Sodium Citrate pH 5.0, 10% PEG 20000, 5mM ApCpp, 2mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23093 / % possible obs: 91.6 % / Redundancy: 7.7 % / Net I/σ(I): 14.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPmodel building
RefinementResolution: 2→32.855 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.64 / Phase error: 28.76
RfactorNum. reflection% reflection
Rfree0.297 1120 4.85 %
Rwork0.2332 --
obs0.2363 23091 91.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→32.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 29 81 2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092830
X-RAY DIFFRACTIONf_angle_d1.1793825
X-RAY DIFFRACTIONf_dihedral_angle_d18.6381060
X-RAY DIFFRACTIONf_chiral_restr0.045444
X-RAY DIFFRACTIONf_plane_restr0.005485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0003-2.09130.38941200.37172633X-RAY DIFFRACTION90
2.0913-2.20150.40681530.31512661X-RAY DIFFRACTION92
2.2015-2.33940.33911310.27992690X-RAY DIFFRACTION92
2.3394-2.520.30031390.25632746X-RAY DIFFRACTION94
2.52-2.77350.29361550.23452816X-RAY DIFFRACTION95
2.7735-3.17450.30161360.22882873X-RAY DIFFRACTION96
3.1745-3.99850.26791680.19082919X-RAY DIFFRACTION97
3.9985-32.85980.25911180.19942633X-RAY DIFFRACTION81

+
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://pdbjlvh1.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