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- PDB-5a43: Crystal structure of a dual topology fluoride ion channel. -

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Basic information

Entry
Database: PDB / ID: 5a43
TitleCrystal structure of a dual topology fluoride ion channel.
Components
  • MONOBODIES
  • PUTATIVE FLUORIDE ION TRANSPORTER CRCB
KeywordsTRANSPORT PROTEIN / FLUORIDE ION CHANNEL / FLUC / EC2
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 / Fluoride-specific ion channel FluC
Similarity search - Component
Biological speciesESCHERICHIA COLI S88 (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 Å
AuthorsStockbridge, R.B. / Kolmakova-Partensky, L. / Shane, T. / Koide, A. / Koide, S. / Miller, C. / Newstead, S.
CitationJournal: Nature / Year: 2015
Title: Crystal Structures of a Double-Barrelled Fluoride Ion Channel.
Authors: Stockbridge, R.B. / Kolmakova-Partensky, L. / Shane, T. / Koide, A. / Koide, S. / Miller, C. / Newstead, S.
History
DepositionJun 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: MONOBODIES
D: MONOBODIES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,96510
Polymers48,4574
Non-polymers1,5096
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-64.5 kcal/mol
Surface area19720 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-76.7 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.420, 87.420, 146.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7758, -0.149, -0.6131), (-0.139, -0.9075, 0.3964), (-0.6155, 0.3928, 0.6833)-69.8175, -8.0785, -23.6188
2given(-0.7406, -0.1919, -0.644), (-0.1332, -0.8974, 0.4206), (-0.6587, 0.3973, 0.639)-67.4627, -8.382, -24.397

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein PUTATIVE FLUORIDE ION TRANSPORTER CRCB / FLUORIDE CHANNEL


Mass: 13863.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI S88 (bacteria) / Variant: O45\:K1 / Plasmid: PASK-IBA2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B7LI20
#2: Protein MONOBODIES


Mass: 10365.372 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHFT2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)

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Sugars , 1 types, 3 molecules

#4: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 3 types, 22 molecules

#3: Chemical ChemComp-F / FLUORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 6.03 Å3/Da / Density % sol: 79 % / Description: NONE
Crystal growpH: 6 / Details: 29% PEG550 MME, 50 MM LINO3, 100 MM ADA PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 34593 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.3 % / Biso Wilson estimate: 62.65 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.58→24.246 Å / SU ML: 0.45 / σ(F): 1.36 / Phase error: 32.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2642 1796 5.2 %
Rwork0.2235 --
obs0.2258 34583 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.65 Å2
Refinement stepCycle: LAST / Resolution: 2.58→24.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 94 19 3481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013552
X-RAY DIFFRACTIONf_angle_d1.4464867
X-RAY DIFFRACTIONf_dihedral_angle_d14.8491337
X-RAY DIFFRACTIONf_chiral_restr0.051588
X-RAY DIFFRACTIONf_plane_restr0.007564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.64970.44121350.39182506X-RAY DIFFRACTION100
2.6497-2.72760.37641220.33882532X-RAY DIFFRACTION100
2.7276-2.81550.36451450.29262534X-RAY DIFFRACTION100
2.8155-2.91590.3081440.28052511X-RAY DIFFRACTION100
2.9159-3.03250.30641010.25592522X-RAY DIFFRACTION100
3.0325-3.17020.28581370.23342508X-RAY DIFFRACTION100
3.1702-3.3370.24451350.2282529X-RAY DIFFRACTION100
3.337-3.54540.26951340.22582528X-RAY DIFFRACTION100
3.5454-3.81820.25211530.20992506X-RAY DIFFRACTION100
3.8182-4.20070.25631610.19812495X-RAY DIFFRACTION100
4.2007-4.80440.19071510.1752524X-RAY DIFFRACTION100
4.8044-6.03750.22081340.2082529X-RAY DIFFRACTION100
6.0375-24.2470.29561440.22732563X-RAY DIFFRACTION100

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