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- PDB-7kkb: Fluoride channel Fluc-Ec2 mutant S81C with bromide -

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Basic information

Entry
Database: PDB / ID: 7kkb
TitleFluoride channel Fluc-Ec2 mutant S81C 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: 2.9 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)49,61812
Polymers47,9504
Non-polymers1,6688
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: previous structures
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-77 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.170, 87.170, 142.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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

#1: Protein Putative fluoride ion transporter CrcB


Mass: 13599.307 Da / Num. of mol.: 2 / Mutation: S81C
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

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Non-polymers , 4 types, 7 molecules

#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: 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.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.68 Å3/Da / Density % sol: 78.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.1M glycine pH 9 36% 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: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91836 Å / Relative weight: 1
ReflectionResolution: 2.9→46.65 Å / Num. obs: 23623 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.37 / Rpim(I) all: 0.108 / Rrim(I) all: 0.386 / Net I/σ(I): 9.8 / Num. measured all: 295813 / Scaling rejects: 112
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
2.9-3.08133.4964937237850.5920.9923.6352.5100
8.7-46.6512.60.073114449060.9790.0260.0792899.4

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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: 2.9→46.65 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 1118 4.74 %
Rwork0.2211 22461 -
obs0.2229 23579 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.3 Å2 / Biso mean: 68.6302 Å2 / Biso min: 33.55 Å2
Refinement stepCycle: final / Resolution: 2.9→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 104 2 3469
Biso mean--93.24 73.74 -
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
2.9-3.030.33221350.303327972932
3.03-3.190.33181530.259827732926
3.19-3.390.31291510.245527992950
3.39-3.650.30811450.228127982943
3.65-4.020.26341050.198828472952
4.02-4.60.18391330.18528132946
4.6-5.80.2241430.189827962939
5.8-46.650.26331530.244628382991
Refinement TLS params.Method: refined / Origin x: 1.527 Å / Origin y: -42.7316 Å / Origin z: -21.6967 Å
111213212223313233
T0.3502 Å2-0.0451 Å20.0119 Å2-0.4307 Å20.0057 Å2--0.3691 Å2
L4.3783 °2-0.3548 °2-1.0672 °2-0.7732 °20.3163 °2--0.6315 °2
S-0.0474 Å °-0.3937 Å °0.1936 Å °-0.0078 Å °0.0733 Å °0.0478 Å °0.0589 Å °0.0774 Å °-0.0487 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 126
2X-RAY DIFFRACTION1allB1 - 125
3X-RAY DIFFRACTION1allC1 - 96
4X-RAY DIFFRACTION1allD1 - 96
5X-RAY DIFFRACTION1allE1 - 2
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allG1 - 2
8X-RAY DIFFRACTION1allH1 - 2
9X-RAY DIFFRACTION1allI201
10X-RAY DIFFRACTION1allJ401 - 501

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