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Yorodumi- PDB-1kpl: Crystal Structure of the ClC Chloride Channel from S. typhimurium -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kpl | ||||||
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Title | Crystal Structure of the ClC Chloride Channel from S. typhimurium | ||||||
Components | putative ClC family, chlorine transport protein | ||||||
Keywords | MEMBRANE 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 | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å | ||||||
Authors | Dutzler, R. / Campbell, E.B. / Cadene, M. / Chait, B.T. / MacKinnon, R. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kpl.cif.gz | 326.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kpl.ent.gz | 269.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kpl_validation.pdf.gz | 498.7 KB | Display | wwPDB validaton report |
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Full document | 1kpl_full_validation.pdf.gz | 578.8 KB | Display | |
Data in XML | 1kpl_validation.xml.gz | 69.3 KB | Display | |
Data in CIF | 1kpl_validation.cif.gz | 92.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/1kpl ftp://data.pdbj.org/pub/pdb/validation_reports/kp/1kpl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | The 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. |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | 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 / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.78 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: BRANDEIS / Detector: CCD / Date: Oct 3, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method 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.
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Displacement parameters | Biso mean: 79.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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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
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LS refinement shell | *PLUS Rfactor Rfree: 0.386 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.361 |