[English] 日本語
Yorodumi
- PDB-7kka: Fluoride channel Fluc-Ec2 mutant S81A with bromide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kka
TitleFluoride channel Fluc-Ec2 mutant S81A with bromide
Components
  • Putative fluoride ion transporter CrcB
  • monobody
KeywordsMEMBRANE PROTEIN / fluoride channel
Function / homology
Function and homology information


fluoride channel activity / cellular detoxification of fluoride / metal ion binding / plasma membrane
Similarity search - Function
Putative fluoride ion transporter CrcB / CrcB-like protein, Camphor Resistance (CrcB) / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BROMIDE ION / FLUORIDE ION / Fluoride-specific ion channel FluC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMcIlwain, B.C. / Stockbridge, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2021
Title: The fluoride permeation pathway and anion recognition in Fluc family fluoride channels.
Authors: McIlwain, B.C. / Gundepudi, R. / Koff, B.B. / Stockbridge, R.B.
History
DepositionOct 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative fluoride ion transporter CrcB
B: Putative fluoride ion transporter CrcB
C: monobody
D: monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,61812
Polymers47,9504
Non-polymers1,6688
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: previously solved structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-71 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.391, 87.391, 141.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

-
Protein / Antibody / Sugars , 3 types, 7 molecules ABCD

#1: Protein Putative fluoride ion transporter CrcB


Mass: 13599.307 Da / Num. of mol.: 2 / Mutation: S81A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: crcB, crcB_2, flc_2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6J5N4
#2: Antibody monobody


Mass: 10375.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#6: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

-
Non-polymers , 4 types, 63 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.66 Å3/Da / Density % sol: 78.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.1 glycine pH9 31% PEG 600

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→39.08 Å / Num. obs: 36655 / % possible obs: 99.6 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.041 / Rrim(I) all: 0.152 / Net I/σ(I): 11.9 / Num. measured all: 502931 / Scaling rejects: 229
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.614.11.9145818941170.6110.5251.9861.7100
9.01-39.0813.80.061110678030.9970.0180.06438.598.5

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A43

5a43


Resolution: 2.5→39.08 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 1854 5.07 %
Rwork0.24 34737 -
obs0.2406 36591 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.72 Å2 / Biso mean: 66.7313 Å2 / Biso min: 40.63 Å2
Refinement stepCycle: final / Resolution: 2.5→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 104 58 3525
Biso mean--87.55 60.78 -
Num. residues----442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.570.36681270.368727102837100
2.57-2.640.36671450.342326502795100
2.64-2.730.34111450.323926762821100
2.73-2.830.32811320.295126722804100
2.83-2.940.28851390.273326672806100
2.94-3.070.29181670.26992616278399
3.07-3.230.25771470.24262648279598
3.23-3.440.25471250.237426862811100
3.44-3.70.25581250.233827142839100
3.7-4.070.27741400.235326912831100
4.08-4.660.22181660.2092643280999
4.67-5.870.23591440.20032686283099
5.87-39.080.20181520.23472678283098

+
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