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- PDB-6bqo: Structure of a dual topology fluoride channel with monobody S8 -

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Basic information

Entry
Database: PDB / ID: 6bqo
TitleStructure of a dual topology fluoride channel with monobody S8
Components
  • Fluoride ion transporter CrcB
  • Monobody S8
KeywordsMEMBRANE PROTEIN / Fluoride channel / monobody / dual topology
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) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
FLUORIDE ION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Fluoride-specific ion channel FluC
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStockbridge, R.B. / Newstead, S. / McIlwain, B.C.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00-GM111767 United States
Wellcome Trust102890/Z/13/Z United Kingdom
Citation
Journal: Structure / Year: 2018
Title: Cork-in-Bottle Occlusion of Fluoride Ion Channels by Crystallization Chaperones.
Authors: McIlwain, B.C. / Newstead, S. / Stockbridge, R.B.
#1: Journal: To Be Published
Title: Structure of fluoride ion channel Fluc-Bpe in complex with monobody S8
Authors: McIlwain, B.C. / Newstead, S. / Stockbridge, R.B.
History
DepositionNov 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluoride ion transporter CrcB
B: Fluoride ion transporter CrcB
C: Monobody S8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0979
Polymers36,9673
Non-polymers1,1316
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, cross-linking, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-46 kcal/mol
Surface area15660 Å2
MethodPISA
2
A: Fluoride ion transporter CrcB
B: Fluoride ion transporter CrcB
C: Monobody S8
hetero molecules

A: Fluoride ion transporter CrcB
B: Fluoride ion transporter CrcB
C: Monobody S8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,19518
Polymers73,9336
Non-polymers2,26112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area13940 Å2
ΔGint-128 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.920, 39.850, 109.870
Angle α, β, γ (deg.)90.00, 107.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Fluoride ion transporter CrcB


Mass: 13291.635 Da / Num. of mol.: 2 / Mutation: E94C, R29K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (bacteria)
Strain: Tohama I / ATCC BAA-589 / NCTC 13251 / Gene: crcB, BP1217 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7VYU0
#2: Protein Monobody S8


Mass: 10383.466 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 53 molecules

#3: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 3.25 Å3/Da / Density % sol: 62.12 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5 / Details: 26% PEG 550MME, 0.1M sodium citrate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→27.969 Å / Num. obs: 11986 / % possible obs: 99.56 % / Redundancy: 8.3 % / Net I/σ(I): 11.68
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NKQ

5nkq


Resolution: 2.8→27.969 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.14
RfactorNum. reflection% reflection
Rfree0.2752 616 5.14 %
Rwork0.2201 --
obs0.2229 11986 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→27.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 42 47 2683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022712
X-RAY DIFFRACTIONf_angle_d0.413713
X-RAY DIFFRACTIONf_dihedral_angle_d9.7151521
X-RAY DIFFRACTIONf_chiral_restr0.034438
X-RAY DIFFRACTIONf_plane_restr0.003447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-3.08190.37321270.30582833X-RAY DIFFRACTION99
3.0819-3.52710.34491640.26142781X-RAY DIFFRACTION100
3.5271-4.4410.2671570.2122850X-RAY DIFFRACTION100
4.441-27.97050.23691680.19132906X-RAY DIFFRACTION99

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