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- PDB-2d4z: Crystal structure of the cytoplasmic domain of the chloride chann... -

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Basic information

Entry
Database: PDB / ID: 2d4z
TitleCrystal structure of the cytoplasmic domain of the chloride channel ClC-0
ComponentsChloride channel protein
KeywordsTRANSPORT PROTEIN / ClC chloride channel cytoplasmic domain / CBS domains / ion channel regulatory subunit
Function / homology
Function and homology information


voltage-gated chloride channel activity / chloride channel complex / plasma membrane
Similarity search - Function
Chloride channel ClC-0 / : / CBS-domain / CBS-domain / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily / CBS domain / CBS domain ...Chloride channel ClC-0 / : / CBS-domain / CBS-domain / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Chloride channel protein
Similarity search - Component
Biological speciesTorpedo marmorata (marbled electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.1 Å
AuthorsDutzler, R. / Meyer, S.
CitationJournal: Structure / Year: 2006
Title: Crystal structure of the cytoplasmic domain of the chloride channel ClC-0.
Authors: Meyer, S. / Dutzler, R.
History
DepositionOct 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 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

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Assembly

Deposited unit
A: Chloride channel protein
B: Chloride channel protein


Theoretical massNumber of molelcules
Total (without water)55,5742
Polymers55,5742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chloride channel protein

B: Chloride channel protein

B: Chloride channel protein


Theoretical massNumber of molelcules
Total (without water)83,3613
Polymers83,3613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area4370 Å2
ΔGint-26 kcal/mol
Surface area26910 Å2
MethodPISA, PQS
3
A: Chloride channel protein

A: Chloride channel protein

A: Chloride channel protein


Theoretical massNumber of molelcules
Total (without water)83,3613
Polymers83,3613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area3990 Å2
ΔGint-18 kcal/mol
Surface area26370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.819, 125.819, 125.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThe biological assembly is probably a dimer. The crystal does not contain the biological assembly.

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Components

#1: Protein Chloride channel protein


Mass: 27786.834 Da / Num. of mol.: 2 / Fragment: ClC-0 cytoplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Torpedo marmorata (marbled electric ray)
Plasmid: pET28 b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P21564

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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 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 3.5M sodium formate 10mM magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.919 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 12312 / Num. obs: 12275 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 72.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 23
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1200 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.1→19.89 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1454756.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE INCLUDES STRETCHES OF WEAK ELECTRON DENSITY WITH ILL DEFINED SIDECHAINS. PARTS OF THE N-TERMINUS AS WELL AS A LINKER REGION HAVE BEEN TRACED AS A POLYGLYCINE CHAIN THEREFORE ...Details: THE STRUCTURE INCLUDES STRETCHES OF WEAK ELECTRON DENSITY WITH ILL DEFINED SIDECHAINS. PARTS OF THE N-TERMINUS AS WELL AS A LINKER REGION HAVE BEEN TRACED AS A POLYGLYCINE CHAIN THEREFORE THESE RESIDUES ARE MISSING ATOMS. SEE REMARK 470. SUBSTANTIAL PARTS OF THE LINKER SHOW NO DEFINED ELECTRON DENSITY; SEE REMARK 465.
RfactorNum. reflection% reflectionSelection details
Rfree0.309 642 5.2 %RANDOM
Rwork0.274 ---
obs0.274 12254 99.9 %-
all-12278 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9256 Å2 / ksol: 0.291994 e/Å3
Displacement parametersBiso mean: 90.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.48 Å
Luzzati d res low-6 Å
Luzzati sigma a0.54 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 0 0 2468
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_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it4.841.5
X-RAY DIFFRACTIONc_mcangle_it8.192
X-RAY DIFFRACTIONc_scbond_it5.022
X-RAY DIFFRACTIONc_scangle_it5.152.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.444 108 5.4 %
Rwork0.393 1908 -
obs--100 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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