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Yorodumi- PDB-2nmr: An unusual twin-His arrangement in the pore of ammonia channels i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nmr | ||||||
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Title | An unusual twin-His arrangement in the pore of ammonia channels is essential for substrate conductance | ||||||
Components | Ammonia channel | ||||||
Keywords | TRANSPORT PROTEIN / Membrane Protein / Ammonia Transport / wild-type AmtB | ||||||
Function / homology | Function and homology information ammonium transmembrane transport / ammonium channel activity / carbon dioxide transport / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lupo, D. / Winkler, F.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance Authors: Javelle, A. / Lupo, D. / Zheng, L. / Li, X.-D. / Winkler, F.K. / Merrick, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nmr.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nmr.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 2nmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nmr_validation.pdf.gz | 437.7 KB | Display | wwPDB validaton report |
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Full document | 2nmr_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 2nmr_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 2nmr_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/2nmr ftp://data.pdbj.org/pub/pdb/validation_reports/nm/2nmr | HTTPS FTP |
-Related structure data
Related structure data | 2nopC 2nowC 2npcC 2npdC 2npeC 2npgC 2npjC 2npkC 1xqfS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44451.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: amtB / Plasmid: pET22b-AmtBLH / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: P69681 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 25% PEG 550, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98007 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2006 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98007 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 33648 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.072 / Net I/σ(I): 13.53 |
Reflection shell | Resolution: 2.1→2.2 Å / Mean I/σ(I) obs: 3.14 / Rsym value: 0.699 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1XQF Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.139 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.123 / 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 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.676 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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