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- PDB-6d0j: Crystal structure of a CLC-type fluoride/proton antiporter -

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Basic information

Entry
Database: PDB / ID: 6d0j
TitleCrystal structure of a CLC-type fluoride/proton antiporter
Components
  • CLC-type fluoride/proton antiporter
  • Monobody
KeywordsTRANSPORT PROTEIN / fluoride/proton antiporter CLC membrane protein
Function / homologyChloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / voltage-gated chloride channel activity / membrane / FLUORIDE ION / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Voltage-gated chloride channel protein
Function and homology information
Biological speciesEnterococcus casseliflavus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLast, N.B. / Stockbridge, R.B. / Wilson, A.E. / Shane, T. / Kolmakova-Partensky, L. / Koide, A. / Koide, S. / Miller, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM107023 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM087519 United States
National Institutes of Health/Office of the DirectorS10OD021832 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: A CLC-type F-/H+antiporter in ion-swapped conformations.
Authors: Last, N.B. / Stockbridge, R.B. / Wilson, A.E. / Shane, T. / Kolmakova-Partensky, L. / Koide, A. / Koide, S. / Miller, C.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 25, 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.funding_organization
Revision 1.4Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLC-type fluoride/proton antiporter
B: CLC-type fluoride/proton antiporter
D: Monobody
C: Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,22515
Polymers111,0634
Non-polymers3,16211
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, Crosslinking demonstrated the homodimeric assembly of the transporter.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-70 kcal/mol
Surface area36060 Å2
Unit cell
Length a, b, c (Å)116.972, 126.421, 133.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUSERSERchain 'A'AA8 - 40211 - 405
211GLUGLUSERSER(chain 'B' and (resid 8 through 244 or (resid 245...BB8 - 40211 - 405
112SERSERVALVAL(chain 'C' and (resid 5 through 12 or resid 14 through 30 or resid 33 through 93))CD5 - 125 - 12
122ALAALASERSER(chain 'C' and (resid 5 through 12 or resid 14 through 30 or resid 33 through 93))CD14 - 3014 - 30
132TYRTYRTHRTHR(chain 'C' and (resid 5 through 12 or resid 14 through 30 or resid 33 through 93))CD33 - 9333 - 93
212SERSERVALVALchain 'D'DC5 - 125 - 12
222ALAALASERSERchain 'D'DC14 - 2914 - 29
232SERSERTHRTHRchain 'D'DC32 - 9332 - 93

NCS ensembles :
ID
1
2

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Components

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Protein / Antibody / Sugars , 3 types, 10 molecules ABDC

#1: Protein CLC-type fluoride/proton antiporter


Mass: 45668.754 Da / Num. of mol.: 2 / Mutation: M4I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (strain EC10) (bacteria)
Strain: EC10 / Gene: ECAG_02710 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9CPP6
#2: Antibody Monobody


Mass: 9862.806 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 3 types, 21 molecules

#4: Chemical
ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: F
#5: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 4.73 Å3/Da / Density % sol: 74.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10 mM HEPES, pH 7.0 100 mM ADA, pH 6.0 100 mM NaF 100 mM K Formate 20% PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2017
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3→49.35 Å / Num. obs: 40496 / % possible obs: 100 % / Redundancy: 34.5 % / Biso Wilson estimate: 126.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.4
Reflection shellResolution: 3→3.12 Å / Redundancy: 32.8 % / Rmerge(I) obs: 3.52 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4523 / CC1/2: 0.825 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q17, 5FXB

3q17

5fxb
PDB Unreleased entry


Resolution: 3→49.35 Å / SU ML: 0.4733 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.5616
RfactorNum. reflection% reflection
Rfree0.2603 1965 4.91 %
Rwork0.2395 --
obs0.2405 39989 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 153.3 Å2
Refinement stepCycle: LAST / Resolution: 3→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7387 0 208 16 7611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00167794
X-RAY DIFFRACTIONf_angle_d0.464810620
X-RAY DIFFRACTIONf_chiral_restr0.03851285
X-RAY DIFFRACTIONf_plane_restr0.00411267
X-RAY DIFFRACTIONf_dihedral_angle_d12.12684497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.43111270.44142705X-RAY DIFFRACTION98.99
3.08-3.160.41311320.40532675X-RAY DIFFRACTION99.26
3.16-3.250.3721370.37032696X-RAY DIFFRACTION98.85
3.25-3.360.40391610.34792670X-RAY DIFFRACTION99.3
3.36-3.480.41431440.30062655X-RAY DIFFRACTION99.29
3.48-3.620.2971550.27472673X-RAY DIFFRACTION98.64
3.62-3.780.31111400.24712667X-RAY DIFFRACTION98.18
3.78-3.980.24571480.23442684X-RAY DIFFRACTION98.23
3.98-4.230.23911460.21422655X-RAY DIFFRACTION97.46
4.23-4.550.23581400.19692712X-RAY DIFFRACTION98.58
4.55-5.010.2321980.18762749X-RAY DIFFRACTION98.89
5.01-5.740.27431050.22032828X-RAY DIFFRACTION99.83
5.74-7.220.23411580.23792769X-RAY DIFFRACTION99.93
7.22-49.350.241740.24042886X-RAY DIFFRACTION99.19
Refinement TLS params.Method: refined / Origin x: 136.274541941 Å / Origin y: 161.797121227 Å / Origin z: 1.43110504995 Å
111213212223313233
T1.25536834833 Å20.0746425770903 Å2-0.108586684914 Å2-1.15835659703 Å2-0.0841261015103 Å2--1.84886129336 Å2
L2.41379911539 °20.0472621057542 °2-0.378001886934 °2-0.554231673902 °20.0616404603883 °2--1.83713783873 °2
S-0.0945924396461 Å °-0.11654201364 Å °0.304377759785 Å °0.0147927286391 Å °0.198385504098 Å °-0.143498832319 Å °-0.00113221458035 Å °0.132039452482 Å °-3.07743452234E-5 Å °
Refinement TLS groupSelection details: all

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