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- PDB-7kkr: Fluoride channel Fluc-Ec2 wild-type with bromide -

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Basic information

Entry
Database: PDB / ID: 7kkr
TitleFluoride channel Fluc-Ec2 wild-type 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 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 28, 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)49,61210
Polymers47,9824
Non-polymers1,6306
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: previous structures solved
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-89 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.620, 87.620, 143.990
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: 13615.307 Da / Num. of mol.: 2
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)
#3: 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
#4: Chemical ChemComp-BR / BROMIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
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: 5.79 Å3/Da / Density % sol: 78.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.1 ADA pH 6.2 0.1 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: 0.9184 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.11→34.42 Å / Num. obs: 19540 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.504 / Rpim(I) all: 0.143 / Rrim(I) all: 0.524 / Net I/σ(I): 7.2 / Num. measured all: 260565 / Scaling rejects: 122
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
3.11-3.3213.92.3814908135260.610.6622.4722100
8.8-34.4213.30.076117198800.9990.0220.07922.498.5

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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: 3.11→34.42 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 902 4.63 %
Rwork0.2375 18598 -
obs0.2392 19500 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.91 Å2 / Biso mean: 46.3545 Å2 / Biso min: 17.71 Å2
Refinement stepCycle: final / Resolution: 3.11→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 228 0 3593
Biso mean--65.39 --
Num. residues----442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.11-3.30.34961500.312830833233100
3.31-3.560.30531470.278930903237100
3.56-3.920.26051570.226431053262100
3.92-4.480.2761470.216630823229100
4.48-5.640.23371350.20223117325299
5.65-34.420.27841660.243331213287100

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