+Open data
-Basic information
Entry | Database: PDB / ID: 3ejy | ||||||
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Title | Structure of E203H mutant of E.coli Cl-/H+ antiporter, CLC-ec1 | ||||||
Components |
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Keywords | IMMUNE SYSTEM/PROTON TRANSPORT / membrane protein / Cl-/H+ exchanger / Antiport / Cell inner membrane / Cell membrane / Chloride / Ion transport / Stress response / Transmembrane / Transport / IMMUNE SYSTEM-PROTON TRANSPORT COMPLEX | ||||||
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: 3.2 Å | ||||||
Authors | Lim, H.-H. / Miller, C. | ||||||
Citation | Journal: J.Gen.Physiol. / Year: 2009 Title: Intracellular proton-transfer mutants in a CLC Cl-/H+ exchanger. Authors: Lim, H.H. / Miller, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ejy.cif.gz | 329.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ejy.ent.gz | 266.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ejy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ejy_validation.pdf.gz | 484.9 KB | Display | wwPDB validaton report |
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Full document | 3ejy_full_validation.pdf.gz | 540.4 KB | Display | |
Data in XML | 3ejy_validation.xml.gz | 63.2 KB | Display | |
Data in CIF | 3ejy_validation.cif.gz | 86.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/3ejy ftp://data.pdbj.org/pub/pdb/validation_reports/ej/3ejy | HTTPS FTP |
-Related structure data
Related structure data | 3ejzC 1otsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 50399.434 Da / Num. of mol.: 2 / Mutation: E203H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clcA, eriC, yadQ, b0155, JW5012 / Production host: Escherichia coli (E. coli) / References: UniProt: P37019 #2: Antibody | Mass: 23693.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma #3: Antibody | Mass: 23088.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma #4: Chemical | ChemComp-BR / Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 37 % PEG 300 (w/v), 20 mM NaBr, 50 mM glycine-NaOH, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.919 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→127 Å / Num. all: 46752 / Num. obs: 46752 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 82.9 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3 / Num. unique all: 6810 / Rsym value: 0.584 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OTS Resolution: 3.2→58.52 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.867 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.5 / 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: 91.344 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→58.52 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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