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

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Basic information

Entry
Database: PDB / ID: 5nkq
TitleCrystal structure of a dual topology fluoride ion channel.
Components
  • Monobody
  • Putative fluoride ion transporter CrcB
KeywordsTRANSPORT PROTEIN / Dual topology channel / Fluoride channel / monobody
Function / homologyfluoride channel activity / cellular detoxification of fluoride / Putative fluoride ion transporter CrcB / CrcB-like protein, Camphor Resistance (CrcB) / metal ion binding / plasma membrane / FLUORIDE ION / Fluoride-specific ion channel FluC
Function and homology information
Biological speciesBordetella pertussis (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsStockbridge, R. / Miller, C. / Newstead, S.
Funding support United Kingdom, United States, 4items
OrganizationGrant numberCountry
Wellcome Trust102890/Z/13/Z United Kingdom
National Institutes of HealthRO1-GM107023 United States
National Institutes of HealthU54-GM087519 United States
National Institutes of HealthK99-GM-111767 United States
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
DepositionMar 31, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionApr 26, 2017ID: 5FXB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: 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: Putative fluoride ion transporter CrcB
B: Putative fluoride ion transporter CrcB
C: Putative fluoride ion transporter CrcB
D: Putative fluoride ion transporter CrcB
E: Monobody
F: Monobody
G: Monobody
H: Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,81718
Polymers93,6198
Non-polymers19810
Water5,008278
1
A: Putative fluoride ion transporter CrcB
B: Putative fluoride ion transporter CrcB
F: Monobody
H: Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9089
Polymers46,8094
Non-polymers995
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Putative fluoride ion transporter CrcB
D: Putative fluoride ion transporter CrcB
E: Monobody
G: Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9089
Polymers46,8094
Non-polymers995
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.590, 84.060, 85.960
Angle α, β, γ (deg.)109.41, 101.40, 101.37
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative fluoride ion transporter CrcB


Mass: 13291.635 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: crcB, BP1217 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7VYU0
#2: Antibody
Monobody /


Mass: 10113.100 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: F
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5.5
Details: 2-26% (V/V) POLYETHYLENE GLYCOL 500 DME, 0.1 M NA-CITRATE PH 5.5, 10 MM NAF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→41 Å / Num. obs: 51576 / % possible obs: 96.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 40.28 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.43 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A40

5a40


Resolution: 2.17→40.952 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.88
RfactorNum. reflection% reflection
Rfree0.2429 2562 4.97 %
Rwork0.2166 --
obs0.2179 51554 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.17→40.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 10 278 6687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026581
X-RAY DIFFRACTIONf_angle_d0.4219030
X-RAY DIFFRACTIONf_dihedral_angle_d9.3763684
X-RAY DIFFRACTIONf_chiral_restr0.0371064
X-RAY DIFFRACTIONf_plane_restr0.0031085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.21170.3291460.28842694X-RAY DIFFRACTION96
2.2117-2.25690.33121600.30282725X-RAY DIFFRACTION96
2.2569-2.3060.35171460.28842649X-RAY DIFFRACTION97
2.306-2.35960.31621290.28952710X-RAY DIFFRACTION95
2.3596-2.41860.3461220.27342711X-RAY DIFFRACTION96
2.4186-2.4840.28761230.26582717X-RAY DIFFRACTION96
2.484-2.55710.30831050.24782763X-RAY DIFFRACTION96
2.5571-2.63960.31751610.22942713X-RAY DIFFRACTION97
2.6396-2.73390.25991560.23052699X-RAY DIFFRACTION97
2.7339-2.84330.2521750.22452688X-RAY DIFFRACTION97
2.8433-2.97270.21811610.20752730X-RAY DIFFRACTION98
2.9727-3.12940.22111450.20062759X-RAY DIFFRACTION98
3.1294-3.32540.23921470.19462734X-RAY DIFFRACTION98
3.3254-3.5820.20721540.20492778X-RAY DIFFRACTION98
3.582-3.94220.25911610.19792725X-RAY DIFFRACTION98
3.9422-4.5120.22021510.21082728X-RAY DIFFRACTION97
4.512-5.68230.20841220.2032717X-RAY DIFFRACTION97
5.6823-40.95960.2037980.19842752X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -5.8456 Å / Origin y: -50.4237 Å / Origin z: 18.2977 Å
111213212223313233
T0.3082 Å20.0005 Å20.011 Å2-0.3107 Å20.037 Å2--0.3822 Å2
L0.0317 °20.0134 °20.0365 °2-0.1689 °20.1021 °2--0.3656 °2
S-0.01 Å °0.0171 Å °0.0116 Å °-0.0159 Å °-0.0051 Å °-0.0404 Å °-0.0215 Å °0.0466 Å °0.0122 Å °
Refinement TLS groupSelection details: all

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