+Open data
-Basic information
Entry | Database: PDB / ID: 4lml | ||||||
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Title | GLIC double mutant I9'A T25'A | ||||||
Components | Proton-gated ion channel | ||||||
Keywords | TRANSPORT PROTEIN / pentameric ligand-gated ion channel / membrane protein / prokaryotic CYS-loop receptor | ||||||
Function / homology | Function and homology information sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane transporter complex / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gloeobacter violaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Grosman, C. / Gonzalez-Gutierrez, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography. Authors: Gonzalez-Gutierrez, G. / Cuello, L.G. / Nair, S.K. / Grosman, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lml.cif.gz | 311.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lml.ent.gz | 257.4 KB | Display | PDB format |
PDBx/mmJSON format | 4lml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lml_validation.pdf.gz | 470.7 KB | Display | wwPDB validaton report |
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Full document | 4lml_full_validation.pdf.gz | 502.7 KB | Display | |
Data in XML | 4lml_validation.xml.gz | 55 KB | Display | |
Data in CIF | 4lml_validation.cif.gz | 74.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/4lml ftp://data.pdbj.org/pub/pdb/validation_reports/lm/4lml | HTTPS FTP |
-Related structure data
Related structure data | 4lmjC 4lmkC 3ehzS C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS domain: (Details: chain E) / NCS domain segments: (Selection details: chain 'E') |
-Components
#1: Protein | Mass: 36292.703 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: I275A,T291A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glvI, glr4197 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7NDN8 |
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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: 4.12 Å3/Da / Density % sol: 70.16 % Description: RPIM = 0.06 (0.337 FOR HIGHEST RESOLUTION SHELL) |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 10-12% PEG4000, 225 mM ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Wavelength: 0.97857 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→44.12 Å / Num. obs: 24202 / % possible obs: 97.2 % / Redundancy: 14 % / Biso Wilson estimate: 24.05 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 12 |
Reflection shell | Highest resolution: 3.8 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.239 / Mean I/σ(I) obs: 1.9 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EHZ Resolution: 3.8→38.932 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.54 / σ(F): 0 / Phase error: 29.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 191.19 Å2 / Biso mean: 53.4301 Å2 / Biso min: 9.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→38.932 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 7427 / Type: POSITIONAL / Rms dev position: 6.174 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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