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- PDB-4kk5: Structure of the CLC-ec1 deltaNC construct in 20mM fluoride and 2... -

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Basic information

Entry
Database: PDB / ID: 4kk5
TitleStructure of the CLC-ec1 deltaNC construct in 20mM fluoride and 20mM bromide
Components
  • Fab, heavy chain
  • Fab, light chain
  • H(+)/Cl(-) exchange transporter ClcA
KeywordsTRANSPORT PROTEIN / membrane transporter / fluoride / bromide
Function / homology
Function and homology information


cellular stress response to acidic pH / chloride:proton antiporter activity / voltage-gated chloride channel activity / proton transmembrane transport / chloride transmembrane transport / B cell differentiation / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin kappa constant / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.171 Å
AuthorsLim, H.-H. / Miller, C.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Fluoride-dependent interruption of the transport cycle of a CLC Cl(-)/H(+) antiporter.
Authors: Lim, H.H. / Stockbridge, R.B. / Miller, C.
History
DepositionMay 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA
C: Fab, heavy chain
D: Fab, light chain
E: Fab, heavy chain
F: Fab, light chain


Theoretical massNumber of molelcules
Total (without water)189,0606
Polymers189,0606
Non-polymers00
Water00
1
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA


Theoretical massNumber of molelcules
Total (without water)95,2372
Polymers95,2372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-46 kcal/mol
Surface area30210 Å2
MethodPISA
2
C: Fab, heavy chain
D: Fab, light chain


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-23 kcal/mol
Surface area19410 Å2
MethodPISA
3
E: Fab, heavy chain
F: Fab, light chain


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-24 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.127, 98.166, 169.761
Angle α, β, γ (deg.)90.00, 131.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H(+)/Cl(-) exchange transporter ClcA / ClC-ec1


Mass: 47618.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0155, clcA, eriC, JW5012, yadQ / Production host: Escherichia coli (E. coli) / References: UniProt: P37019
#2: Antibody Fab, heavy chain


Mass: 23823.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: MUS MUSCULUS (house mouse)
#3: Antibody Fab, light chain


Mass: 23088.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: MUS MUSCULUS (house mouse) / References: UniProt: P01837*PLUS
Has protein modificationY

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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: 3.77 Å3/Da / Density % sol: 67.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100mM Na/K tartrate, 26%PEG400, 100mM Glycine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 3.17→40 Å / Num. all: 91644 / Num. obs: 91572 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.171→39.782 Å / SU ML: 0.35 / σ(F): 1.94 / σ(I): 2 / Phase error: 30.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 2383 5.08 %random
Rwork0.232 ---
obs0.2339 91572 97.9 %-
all-91644 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.171→39.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13223 0 0 0 13223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613551
X-RAY DIFFRACTIONf_angle_d0.81418436
X-RAY DIFFRACTIONf_dihedral_angle_d13.6074768
X-RAY DIFFRACTIONf_chiral_restr0.0512121
X-RAY DIFFRACTIONf_plane_restr0.0042314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1713-3.20740.40461220.35921993X-RAY DIFFRACTION68
3.2074-3.24510.35941600.34362804X-RAY DIFFRACTION94
3.2451-3.28460.33231350.32182861X-RAY DIFFRACTION95
3.2846-3.32620.34781620.32282832X-RAY DIFFRACTION98
3.3262-3.36990.4091260.3232993X-RAY DIFFRACTION98
3.3699-3.41610.33061740.30072833X-RAY DIFFRACTION99
3.4161-3.46490.32792090.28582945X-RAY DIFFRACTION99
3.4649-3.51650.31821560.27922899X-RAY DIFFRACTION99
3.5165-3.57150.31121630.25672943X-RAY DIFFRACTION99
3.5715-3.630.34711440.26862931X-RAY DIFFRACTION99
3.63-3.69250.27931580.26372932X-RAY DIFFRACTION99
3.6925-3.75960.33781680.25222943X-RAY DIFFRACTION99
3.7596-3.83190.30591700.25342888X-RAY DIFFRACTION99
3.8319-3.910.30041410.23852985X-RAY DIFFRACTION99
3.91-3.9950.27431380.23592971X-RAY DIFFRACTION99
3.995-4.08780.31511640.2422910X-RAY DIFFRACTION99
4.0878-4.18990.28241770.21852908X-RAY DIFFRACTION99
4.1899-4.30310.25941470.21692981X-RAY DIFFRACTION99
4.3031-4.42950.24961370.21032949X-RAY DIFFRACTION99
4.4295-4.57230.22951410.20312941X-RAY DIFFRACTION100
4.5723-4.73550.23461750.20162936X-RAY DIFFRACTION100
4.7355-4.92480.23881430.19422986X-RAY DIFFRACTION100
4.9248-5.14840.23891590.20432930X-RAY DIFFRACTION100
5.1484-5.41930.27171670.20042971X-RAY DIFFRACTION99
5.4193-5.75790.24851370.20112930X-RAY DIFFRACTION100
5.7579-6.20090.26221540.21472967X-RAY DIFFRACTION100
6.2009-6.82210.24781650.20092924X-RAY DIFFRACTION100
6.8221-7.80280.19591520.182970X-RAY DIFFRACTION100
7.8028-9.80630.17751660.16732942X-RAY DIFFRACTION100
9.8063-39.78520.30231450.28342919X-RAY DIFFRACTION98

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