[English] 日本語
Yorodumi
- PDB-6uru: iAChSnFR Fluorescent Acetylcholine Sensor precursor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uru
TitleiAChSnFR Fluorescent Acetylcholine Sensor precursor
ComponentsiAChSnFR precursor
KeywordsFLUORESCENT PROTEIN / Biosensor / sensor / neurotransmitter / acetylcholine / circularly permuted
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBorden, P.M. / Marvin, J.S. / Looger, L.L.
CitationJournal: To Be Published
Title: iAChSnFR Fluorescent Acetylcholine Sensor precursor
Authors: Borden, P.M. / Marvin, J.S. / Looger, L.L.
History
DepositionOct 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 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: iAChSnFR precursor
B: iAChSnFR precursor


Theoretical massNumber of molelcules
Total (without water)125,7942
Polymers125,7942
Non-polymers00
Water00
1
A: iAChSnFR precursor


Theoretical massNumber of molelcules
Total (without water)62,8971
Polymers62,8971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: iAChSnFR precursor


Theoretical massNumber of molelcules
Total (without water)62,8971
Polymers62,8971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.120, 89.780, 92.890
Angle α, β, γ (deg.)90.000, 90.480, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein iAChSnFR precursor


Mass: 62896.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Phosphate buffer

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→92.9 Å / Num. obs: 36373 / % possible obs: 99.3 % / Redundancy: 5.1 % / CC1/2: 0.989 / Rmerge(I) obs: 0.141 / Net I/σ(I): 8
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 1.228 / Num. unique obs: 5167 / CC1/2: 0.299

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5f9g, 3ppn

5f9g

3ppn


Resolution: 2.6→92.89 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 15.025 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.976 / ESU R Free: 0.337
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 1724 4.7 %RANDOM
Rwork0.2135 ---
obs0.2159 34575 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 177.77 Å2 / Biso mean: 53.719 Å2 / Biso min: 26.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0.07 Å2
2--0.46 Å20 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 2.6→92.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 3370 0 11344
Biso mean--50.22 --
Num. residues----560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0158148
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177518
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.75511016
X-RAY DIFFRACTIONr_angle_other_deg0.4881.71217624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4885994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88821.825252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.807151238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2281522
X-RAY DIFFRACTIONr_chiral_restr0.0580.21054
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218994
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021462
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 105 -
Rwork0.333 2486 -
all-2591 -
obs--95.86 %

+
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