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- PDB-1kpk: Crystal Structure of the ClC Chloride Channel from E. coli -

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Basic information

Entry
Database: PDB / ID: 1kpk
TitleCrystal Structure of the ClC Chloride Channel from E. coli
Componentsputative channel transporter
KeywordsMEMBRANE PROTEIN / helical membrane protein / homodimer
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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsDutzler, R. / Campbell, E.B. / Cadene, M. / Chait, B.T. / MacKinnon, R.
CitationJournal: Nature / Year: 2002
Title: X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity.
Authors: Dutzler, R. / Campbell, E.B. / Cadene, M. / Chait, B.T. / MacKinnon, R.
History
DepositionDec 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: putative channel transporter
B: putative channel transporter
C: putative channel transporter
D: putative channel transporter
E: putative channel transporter
F: putative channel transporter


Theoretical massNumber of molelcules
Total (without water)302,3426
Polymers302,3426
Non-polymers00
Water00
1
A: putative channel transporter
B: putative channel transporter


Theoretical massNumber of molelcules
Total (without water)100,7812
Polymers100,7812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: putative channel transporter
D: putative channel transporter


Theoretical massNumber of molelcules
Total (without water)100,7812
Polymers100,7812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: putative channel transporter
F: putative channel transporter


Theoretical massNumber of molelcules
Total (without water)100,7812
Polymers100,7812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.660, 152.525, 263.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99996, -0.00895, 0.00121), (0.00493, -0.42854, 0.90351), (-0.00757, 0.90348, 0.42857)69.65647, 19.90589, -12.34595
3given(0.99998, 0.0044, 0.00419), (-0.0043, 0.99975, -0.02199), (-0.00429, 0.02198, 0.99975)-0.35898, -11.35713, 166.48964
4given(-0.99995, -0.00705, 0.00697), (0.00939, -0.44828, 0.89385), (-0.00317, 0.89387, 0.44832)69.33211, 8.51616, 154.28549
5given(0.99991, 0.00967, 0.0098), (-0.01362, 0.59081, 0.8067), (0.00201, -0.80675, 0.59088)17.48277, 49.93853, 7.5917
6given(-0.99989, -0.00423, 0.01414), (0.01042, 0.47576, 0.87951), (-0.01045, 0.87956, -0.47567)87.20429, 50.79093, -15.62315
DetailsThe biologically active assembly is a homodimer. The three biological dimers in the asymmetric unit are composed of protein chains A and B, C and D, and E and F.

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Components

#1: Protein
putative channel transporter / ClC chloride channel subunit


Mass: 50390.402 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yadQ / Plasmid: pET28b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P37019

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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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 400, tris, sodium sulfate, lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110-15 mg/mlprotein1drop
245 mMn-octyl-beta-maltoside1drop
375 mM1dropNaCl
410 mMTris-HCl1droppH7.5
531-34 %PEG4001reservoir
650 mMTris1reservoirpH8.5
750 mM1reservoirNa2SO4
850 mM1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.782 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 55065 / Num. obs: 54294 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 85.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 26.3
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4938 / % possible all: 91.3
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 91.3 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4749113.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Strict 6-fold NCS constraints were maintained during refinement. BULK SOLVENT MODEL USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.301 5321 9.9 %RANDOM
Rwork0.29 ---
all0.2912 54088 --
obs0.29 53763 99.4 %-
Displacement parametersBiso mean: 104.9 Å2
Baniso -1Baniso -2Baniso -3
1-24.09 Å20 Å20 Å2
2---13.68 Å20 Å2
3----10.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.57 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20274 0 0 0 20274
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.972
X-RAY DIFFRACTIONc_scbond_it5.793
X-RAY DIFFRACTIONc_scangle_it8.075
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.418 874 10 %
Rwork0.4 7884 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.29 / Rfactor Rfree: 0.302 / Rfactor Rwork: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 104.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_scbond_it5.793
X-RAY DIFFRACTIONc_mcangle_it2.972
X-RAY DIFFRACTIONc_scangle_it8.075
LS refinement shell
*PLUS
Rfactor Rfree: 0.418 / % reflection Rfree: 10 % / Rfactor Rwork: 0.4

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