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- PDB-6d0n: Crystal structure of a CLC-type fluoride/proton antiporter, V319G... -

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Basic information

Entry
Database: PDB / ID: 6d0n
TitleCrystal structure of a CLC-type fluoride/proton antiporter, V319G mutant
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: 3.12 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, 2items
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
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)114,14212
Polymers111,0374
Non-polymers3,1058
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, Cross-linking demonstrated homodimeric nature of transporter.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.106, 124.843, 135.482
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-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'C' and (resid 5 through 12 or resid 14 through 93))C8 - 402
211chain 'D'D8 - 402
112chain 'A'A5 - 12
122chain 'A'A14 - 93
212(chain 'B' and (resid 8 through 244 or (resid 245...B5 - 12
222(chain 'B' and (resid 8 through 244 or (resid 245...B14 - 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: 45626.676 Da / Num. of mol.: 2 / Mutation: M4I, V319G
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: 9891.871 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, 13 molecules

#4: Chemical ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#5: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID / ADA (buffer)


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


Mass: 18.015 Da / Num. of mol.: 11 / 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: 4.77 Å3/Da / Density % sol: 74.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 10 mM HEPES, pH 7.0 100 mM ADA, pH 6.2 100 mM NaF 100 mM K Formate 24% PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 29, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.12→49.67 Å / Num. obs: 36328 / % possible obs: 99.9 % / Redundancy: 17.6 % / Biso Wilson estimate: 124.36 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.2
Reflection shellResolution: 3.12→3.26 Å / Redundancy: 17.3 % / Rmerge(I) obs: 2.81 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4328 / CC1/2: 0.699 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D0J

6d0j


Resolution: 3.12→49.67 Å / SU ML: 0.5165 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.6874 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2701 1778 4.95 %
Rwork0.2483 34111 -
obs0.2494 35889 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 169.94 Å2
Refinement stepCycle: LAST / Resolution: 3.12→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7398 0 205 11 7614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00167806
X-RAY DIFFRACTIONf_angle_d0.451610635
X-RAY DIFFRACTIONf_chiral_restr0.03871284
X-RAY DIFFRACTIONf_plane_restr0.00421270
X-RAY DIFFRACTIONf_dihedral_angle_d12.30274504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.20.49551280.4642581X-RAY DIFFRACTION99.01
3.2-3.30.4811390.45252596X-RAY DIFFRACTION99.45
3.3-3.410.42351600.41662571X-RAY DIFFRACTION99.2
3.41-3.530.37061440.33612588X-RAY DIFFRACTION99.31
3.53-3.670.34661270.29872618X-RAY DIFFRACTION99.31
3.67-3.840.30291570.26362583X-RAY DIFFRACTION98.88
3.84-4.040.22321440.23732558X-RAY DIFFRACTION98.54
4.04-4.290.24691350.2232596X-RAY DIFFRACTION97.4
4.29-4.620.26451250.18892589X-RAY DIFFRACTION97.59
4.62-5.090.2136940.1882660X-RAY DIFFRACTION98.67
5.09-5.820.28651030.21542698X-RAY DIFFRACTION99.68
5.82-7.330.2311610.2392689X-RAY DIFFRACTION99.86
7.33-49.670.25091610.2452784X-RAY DIFFRACTION98.93
Refinement TLS params.Method: refined / Origin x: 137.770267351 Å / Origin y: 159.593966428 Å / Origin z: 1.70189385981 Å
111213212223313233
T1.10377615294 Å20.0598671400562 Å2-0.0837396240863 Å2-1.06302045682 Å2-0.0696510971052 Å2--2.14014944364 Å2
L2.58839225773 °20.123405514012 °2-0.303986645268 °2-0.742897511937 °20.0963454408317 °2--2.81789425876 °2
S0.0880968505328 Å °-0.198295824939 Å °0.231215254739 Å °0.0418905854109 Å °0.0290684228938 Å °-0.215991646089 Å °-0.0294398872568 Å °0.262997417339 Å °0.00834115968477 Å °
Refinement TLS groupSelection details: all

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