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- PDB-2pfi: Crystal structure of the cytoplasmic domain of the human chloride... -

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Basic information

Entry
Database: PDB / ID: 2pfi
TitleCrystal structure of the cytoplasmic domain of the human chloride channel ClC-Ka
ComponentsChloride channel protein ClC-Ka
KeywordsTRANSPORT PROTEIN / Cystathionine beta synthetase (CBS) domains containing protein
Function / homology
Function and homology information


excretion / voltage-gated chloride channel activity / regulation of monoatomic ion transmembrane transport / chloride transport / plasma membrane => GO:0005886 / chloride channel complex / monoatomic ion transmembrane transport / Stimuli-sensing channels / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Chloride channel ClC-K / CBS-domain / CBS-domain / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. ...Chloride channel ClC-K / CBS-domain / CBS-domain / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Chloride channel protein ClC-Ka
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsMarkovic, S. / Dutzler, R.
CitationJournal: Structure / Year: 2007
Title: The Structure of the Cytoplasmic Domain of the Chloride Channel ClC-Ka Reveals a Conserved Interaction Interface.
Authors: Markovic, S. / Dutzler, R.
History
DepositionApr 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Remark 999SEQUENCE THE SEQUENCE WAS CLONED WITH C-TERMINAL RECOGNITION SITE FOR PRESCISSION PROTEASE FOLLOWED ...SEQUENCE THE SEQUENCE WAS CLONED WITH C-TERMINAL RECOGNITION SITE FOR PRESCISSION PROTEASE FOLLOWED BY A HEXA-HISTIDINE TAG THAT WAS CLEAVED OFF DURING PURIFICATION

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chloride channel protein ClC-Ka
B: Chloride channel protein ClC-Ka
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5336
Polymers36,3002
Non-polymers2334
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-41 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.283, 83.421, 59.888
Angle α, β, γ (deg.)90.00, 92.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chloride channel protein ClC-Ka / / Chloride channel Ka / ClC-K1


Mass: 18149.816 Da / Num. of mol.: 2 / Fragment: human ClC-Ka C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLCNKA / Plasmid: pet 28b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21/DE3 / References: UniProt: P51800
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 4000, 100mM KI, 60mM Tris-HCl, 150mM NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 45049 / Num. obs: 43653 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 26.9
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2317 / % possible all: 79

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→14.89 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 820085.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 4198 9.6 %RANDOM
Rwork0.2 ---
obs0.2 43605 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.979 Å2 / ksol: 0.406422 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å2-1.88 Å2
2--0.89 Å20 Å2
3----0.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→14.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 4 286 2573
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.862.5
X-RAY DIFFRACTIONc_mcangle_it2.693.5
X-RAY DIFFRACTIONc_scbond_it4.745.5
X-RAY DIFFRACTIONc_scangle_it6.737
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 515 8.5 %
Rwork0.27 5538 -
obs--80.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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