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- PDB-1kpl: Crystal Structure of the ClC Chloride Channel from S. typhimurium -

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Basic information

Entry
Database: PDB / ID: 1kpl
TitleCrystal Structure of the ClC Chloride Channel from S. typhimurium
Componentsputative ClC family, chlorine transport protein
KeywordsMEMBRANE PROTEIN / helical membrane protein / homodimer / ion channel
Function / homology
Function and homology information


: / voltage-gated chloride channel activity / chloride ion binding / plasma membrane => GO:0005886 / 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
PENTADECANE / N-OCTANE / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 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 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative ClC family, chlorine transport protein
B: putative ClC family, chlorine transport protein
C: putative ClC family, chlorine transport protein
D: putative ClC family, chlorine transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,17816
Polymers201,9984
Non-polymers1,17912
Water362
1
A: putative ClC family, chlorine transport protein
B: putative ClC family, chlorine transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6859
Polymers100,9992
Non-polymers6867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: putative ClC family, chlorine transport protein
D: putative ClC family, chlorine transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4937
Polymers100,9992
Non-polymers4945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.719, 90.159, 80.753
Angle α, β, γ (deg.)90.00, 98.95, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.87657, 0.48126, 0.0038), (0.48002, 0.87481, -0.06545), (-0.03483, -0.05555, -0.99785)62.70105, -15.74265, 5.73088
DetailsThe biologically active assembly is a homodimer. The two biological dimers in the asymmetric unit are composed of protein chains A and B, C and D. Strict crystallograhic NCS constraints have been maintained between the two dimers in the asymmetric unit.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
putative ClC family, chlorine transport protein / ClC chloride channel


Mass: 50499.586 Da / Num. of mol.: 4 / Mutation: M26L/C264V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pET28b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q8ZRP8

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Non-polymers , 5 types, 14 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-MYS / PENTADECANE / Pentadecane


Mass: 212.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H32
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG 400, acetate, sodium sulfate, lithium sulfate, pH 4.6, 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
526-31 %PEG4001reservoir
650 mMsodium acetate1reservoirpH4.6
775-100 mM1reservoirNa2SO4
875-100 mM1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Oct 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. all: 53397 / Num. obs: 50567 / % possible obs: 94.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 85.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.7
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 1.7 / % possible all: 96.6
Reflection shell
*PLUS
% possible obs: 96.6 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1592586.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Strict 2-fold NCS constraints between the two dimers in the asymmetric unit were maintained. BULK SOLVENT MODEL USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 4981 10 %RANDOM
Rwork0.254 ---
all0.2583 52912 --
obs0.255 49949 94.4 %-
Displacement parametersBiso mean: 79.6 Å2
Baniso -1Baniso -2Baniso -3
1-26.57 Å20 Å2-11.87 Å2
2--5.33 Å20 Å2
3----31.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13144 0 70 2 13216
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it6.754
X-RAY DIFFRACTIONc_scangle_it9.056
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 808 9.7 %
Rwork0.361 7552 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3ALKANE.PARALKANE.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 79.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_scbond_it6.754
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scangle_it9.056
LS refinement shell
*PLUS
Rfactor Rfree: 0.386 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.361

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