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- PDB-6d0k: Crystal structure of a CLC-type fluoride/proton antiporter, E118Q... -

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Basic information

Entry
Database: PDB / ID: 6d0k
TitleCrystal structure of a CLC-type fluoride/proton antiporter, E118Q 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: 3.35 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)114,22315
Polymers111,0614
Non-polymers3,16211
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, Cross-linking demonstrated dimeric state of transporter.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-70 kcal/mol
Surface area36040 Å2
Unit cell
Length a, b, c (Å)118.323, 125.987, 134.079
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: 45667.770 Da / Num. of mol.: 2 / Mutation: M4I, E118Q
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, 14 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.: 9 / 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: 4.78 Å3/Da / Density % sol: 74.24 %
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: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 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: 3.35→49.73 Å / Num. obs: 29497 / % possible obs: 99.8 % / Redundancy: 8.4 % / Biso Wilson estimate: 162.14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.5
Reflection shellResolution: 3.35→3.55 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.905 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4638 / CC1/2: 0.649 / % possible all: 99.2

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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: 3.35→49.73 Å / SU ML: 0.4703 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.6084
RfactorNum. reflection% reflection
Rfree0.2661 1442 4.93 %
Rwork0.2443 --
obs0.2453 29271 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 192.62 Å2
Refinement stepCycle: LAST / Resolution: 3.35→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7387 0 208 9 7604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00167794
X-RAY DIFFRACTIONf_angle_d0.461710620
X-RAY DIFFRACTIONf_chiral_restr0.03851285
X-RAY DIFFRACTIONf_plane_restr0.00421267
X-RAY DIFFRACTIONf_dihedral_angle_d12.1224497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.470.42851600.40242721X-RAY DIFFRACTION99.48
3.47-3.610.38561450.3372742X-RAY DIFFRACTION99.38
3.61-3.770.3581400.28352740X-RAY DIFFRACTION99.34
3.77-3.970.26571600.25342726X-RAY DIFFRACTION99.28
3.97-4.220.31141480.23282742X-RAY DIFFRACTION98.84
4.22-4.550.26131460.20712765X-RAY DIFFRACTION99.08
4.55-50.21961050.18842805X-RAY DIFFRACTION99.39
5-5.730.27711040.22052841X-RAY DIFFRACTION99.7
5.73-7.210.25781570.24422826X-RAY DIFFRACTION99.93
7.21-49.740.25041770.25232921X-RAY DIFFRACTION99.01
Refinement TLS params.Method: refined / Origin x: 137.841408937 Å / Origin y: 161.131810958 Å / Origin z: 1.51819653091 Å
111213212223313233
T1.57478484154 Å20.0604673085212 Å2-0.183501582836 Å2-1.3445488127 Å20.0236420749239 Å2--2.57862695057 Å2
L2.33519443693 °20.153451943704 °2-0.615440311867 °2-0.285112901115 °2-0.0373788785105 °2--2.16263958582 °2
S0.0652340987456 Å °-0.0932567342512 Å °0.132297902872 Å °-0.0127545713736 Å °0.011580880967 Å °-0.24714361203 Å °-0.034914726498 Å °0.212441955678 Å °-0.000101826837401 Å °
Refinement TLS groupSelection details: all

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