+Open data
-Basic information
Entry | Database: PDB / ID: 5hd8 | |||||||||||||||
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Title | Crystal structure of disulfide cross-linked D417C ClC-ec1 | |||||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN / antiporter / membrane exchanger | |||||||||||||||
Function / homology | Function and homology information chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / chloride transmembrane transport / proton transmembrane transport / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) Mus musculus (house mouse) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | |||||||||||||||
Authors | Mathews, I.I. / Khantwal, C.M. / Maduke, M. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: To be published Title: Conformational change in CLC transporters: beyond the rotation of Gluex Authors: Khantwal, C.M. / Abraham, S.J. / Han, W. / Jiang, T. / Chavan, T.S. / Cheng, R.C. / Elvington, S.M. / Liu, C.W. / Mathews, I.I. / Stein, R.A. / Mchaourab, H.S. / Tajkhorshid, E. / Maduke, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hd8.cif.gz | 658 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hd8.ent.gz | 552.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hd8_validation.pdf.gz | 471.2 KB | Display | wwPDB validaton report |
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Full document | 5hd8_full_validation.pdf.gz | 492.6 KB | Display | |
Data in XML | 5hd8_validation.xml.gz | 56.5 KB | Display | |
Data in CIF | 5hd8_validation.cif.gz | 77.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/5hd8 ftp://data.pdbj.org/pub/pdb/validation_reports/hd/5hd8 | HTTPS FTP |
-Related structure data
Related structure data | 1otsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48034.969 Da / Num. of mol.: 2 / Mutation: D417C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: clcA, eriC, yadQ, b0155, JW5012 / Plasmid: pASK-IBA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37019 #2: Antibody | Mass: 23823.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): ST10C3/G4 / Production host: Mus musculus (house mouse) #3: Antibody | Mass: 23088.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): ST10C3/G4 / Production host: Mus musculus (house mouse) #4: Chemical | ChemComp-CL / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 9 Details: 30% PEG 400, 0.075M K/Na-tartrate, 0.1M Tris.HCl (pH 9.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: used cryostream |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2014 Details: Rh coated collimating mirrors, K-B focusing mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→39.2 Å / Num. obs: 44041 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.76 |
Reflection shell | Resolution: 3.15→3.23 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.74 / % possible all: 80.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OTS Resolution: 3.15→39.2 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.874 / SU B: 45.257 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 105.994 Å2
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Refinement step | Cycle: 1 / Resolution: 3.15→39.2 Å
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