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- PDB-7kk9: Fluoride channel Fluc-Ec2 mutant S81A/T82A with bromide -

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Basic information

Entry
Database: PDB / ID: 7kk9
TitleFluoride channel Fluc-Ec2 mutant S81A/T82A with bromide
Components
  • Putative fluoride ion transporter CrcB
  • monobody
KeywordsMEMBRANE PROTEIN / fluoride channel
Function / homologyfluoride channel activity / cellular detoxification of fluoride / Putative fluoride ion transporter CrcB / CrcB-like protein, Camphor Resistance (CrcB) / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / plasma membrane / BROMIDE ION / Fluoride-specific ion channel FluC
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)49,52010
Polymers47,8904
Non-polymers1,6306
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: previous structures
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-91 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.460, 87.460, 147.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Putative fluoride ion transporter CrcB


Mass: 13569.280 Da / Num. of mol.: 2 / Mutation: S81A,T82A
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.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: 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
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.92 Å3/Da / Density % sol: 79.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.1 M ADA pH 6 0.1M AMSO4 31% PEG 600

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.91836 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91836 Å / Relative weight: 1
ReflectionResolution: 3.1→41.92 Å / Num. obs: 20107 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.73 / Rpim(I) all: 0.202 / Rrim(I) all: 0.758 / Net I/σ(I): 8.5 / Num. measured all: 273453 / Scaling rejects: 259
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
3.1-3.31146.2035075436160.7291.6976.4332.1100
8.77-41.9213.70.071124229050.9980.0220.07525.999.2

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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: 3.1→41.92 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 1052 5.25 %
Rwork0.23 19003 -
obs0.2312 20055 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 258.19 Å2 / Biso mean: 78.7895 Å2 / Biso min: 43.88 Å2
Refinement stepCycle: final / Resolution: 3.1→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 228 0 3587
Biso mean--121.33 --
Num. residues----442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1-3.240.35191420.316123352477
3.24-3.410.40711460.291423452491
3.41-3.630.31681090.26824002509
3.63-3.910.31231300.233523692499
3.91-4.30.27281160.223623982514
4.3-4.920.1971700.188123522522
4.92-6.190.19571080.205923922500
6.19-41.920.21721310.226724122543

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