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- PDB-5a40: Crystal structure of a dual topology fluoride ion channel. -

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Basic information

Entry
Database: PDB / ID: 5a40
TitleCrystal structure of a dual topology fluoride ion channel.
Components
  • MONOBODIES
  • PUTATIVE FLUORIDE ION TRANSPORTER CRCB
KeywordsTRANSPORT PROTEIN / FLUORIDE ION CHANNEL / MONOBODY / BPE
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-specific ion channel FluC
Similarity search - Component
Biological speciesBORDETELLA PERTUSSIS (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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: PUTATIVE FLUORIDE ION TRANSPORTER CRCB
D: PUTATIVE FLUORIDE ION TRANSPORTER CRCB
E: MONOBODIES
F: MONOBODIES
G: MONOBODIES
H: MONOBODIES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,11012
Polymers93,3078
Non-polymers8024
Water00
1
A: PUTATIVE FLUORIDE ION TRANSPORTER CRCB
B: PUTATIVE FLUORIDE ION TRANSPORTER CRCB
E: MONOBODIES
F: MONOBODIES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0556
Polymers46,6544
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-114.5 kcal/mol
Surface area18410 Å2
MethodPISA
2
C: PUTATIVE FLUORIDE ION TRANSPORTER CRCB
D: PUTATIVE FLUORIDE ION TRANSPORTER CRCB
G: MONOBODIES
H: MONOBODIES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0556
Polymers46,6544
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-113.5 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.790, 183.700, 72.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2815, -0.8482, 0.4486), (-0.8465, -0.0006, -0.5324), (0.4519, -0.5296, -0.7179)-64.4082, -10.9005, 82.1158
2given(-0.666, 0.6054, -0.4359), (0.6725, 0.2343, -0.702), (-0.3229, -0.7606, -0.5632)-27.0909, 108.1341, 18.6829
3given(-0.5395, -0.7072, 0.457), (0.7302, -0.1228, 0.6721), (-0.4192, 0.6963, 0.5826)-140.1327, 0.7142, -0.5841
4given(-0.3296, -0.8325, 0.4454), (-0.832, 0.0331, -0.5538), (0.4463, -0.5531, -0.7035)-66.2546, -8.5229, 81.0081
5given(-0.647, 0.6366, -0.4196), (0.6744, 0.221, -0.7045), (-0.3558, -0.7388, -0.5723)-25.793, 108.345, 17.3975
6given(-0.5358, -0.7186, 0.4433), (0.7119, -0.1022, 0.6948), (-0.454, 0.6878, 0.5664)-139.6532, -1.0118, -2.8714

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Components

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


Mass: 13291.635 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BORDETELLA PERTUSSIS (bacteria) / Strain: TOHAMA 1 / Plasmid: PASK-IBA2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7VYU0
#2: Protein
MONOBODIES


Mass: 10035.201 Da / Num. of mol.: 4
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)
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg

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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: 5.39 Å3/Da / Density % sol: 77 % / Description: NONE
Crystal growpH: 8.5
Details: 36-41% PEG 550 MME, 0.2M MGCL, 0.1M TRIS-HCL, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.006
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 3.6→48 Å / Num. obs: 23518 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 83.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 3.6→3.7 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.6 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
SHELXSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.6→114.708 Å / Cor.coef. Fo:Fc: 0.847 / Cor.coef. Fo:Fc free: 0.846 / SU B: 25.286 / SU ML: 0.369 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.73 / ESU R Free: 0.56 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 1134 5.14 %RANDOM
Rwork0.2348 ---
obs0.236 22219 94.188 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 78.589 Å2
Baniso -1Baniso -2Baniso -3
1--0.282 Å20 Å20 Å2
2---0.415 Å20 Å2
3---0.697 Å2
Refinement stepCycle: LAST / Resolution: 3.6→114.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6484 0 4 0 6488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026696
X-RAY DIFFRACTIONr_bond_other_d0.0050.026324
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9449212
X-RAY DIFFRACTIONr_angle_other_deg1.125314471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6975856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19721.714210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.34315923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7411524
X-RAY DIFFRACTIONr_chiral_restr0.0880.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217458
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021546
X-RAY DIFFRACTIONr_nbd_refined0.2410.21746
X-RAY DIFFRACTIONr_nbd_other0.3290.280
X-RAY DIFFRACTIONr_nbtor_refined0.2010.23343
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2185
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9617.7343433
X-RAY DIFFRACTIONr_mcbond_other5.967.7333432
X-RAY DIFFRACTIONr_mcangle_it9.54611.5824280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5338.1383263
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.90312.0784930
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 40 -
Rwork0.279 653 -
obs--40.693 %

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