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Yorodumi- PDB-5bz2: CRYSTAL STRUCTURE OF THE SODIUM PROTON ANTIPORTER NAPA IN INWARD-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bz2 | ||||||
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Title | CRYSTAL STRUCTURE OF THE SODIUM PROTON ANTIPORTER NAPA IN INWARD-FACING CONFORMATION | ||||||
Components | Na(+)/H(+) antiporter | ||||||
Keywords | TRANSPORT PROTEIN / INWARD-FACING / CYSTEIN CROSSLINK | ||||||
Function / homology | Function and homology information antiporter activity / proton transmembrane transport / membrane / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Coincon, M. / Uzdavinys, P. / Cameron, A. / Drew, D. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2016 Title: Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters. Authors: Coincon, M. / Uzdavinys, P. / Nji, E. / Dotson, D.L. / Winkelmann, I. / Abdul-Hussein, S. / Cameron, A.D. / Beckstein, O. / Drew, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bz2.cif.gz | 215.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bz2.ent.gz | 177.5 KB | Display | PDB format |
PDBx/mmJSON format | 5bz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/5bz2 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/5bz2 | HTTPS FTP |
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-Related structure data
Related structure data | 5bz3C 4bwzS 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: 40306.109 Da / Num. of mol.: 1 / Mutation: V31C I130C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT_C1108 / Plasmid: PWALDOGFPE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: Q72IM4, UniProt: Q5SIA2*PLUS |
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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: 4.14 Å3/Da / Density % sol: 70.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.05M glycine pH 9.5, 0.1M NaCl, 34-38% PEG 300 / PH range: 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: LN2 |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→33.64 Å / Num. obs: 7404 / % possible obs: 100 % / Observed criterion σ(I): 13.26 / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.26 |
Reflection shell | Resolution: 3.7→3.832 Å / Redundancy: 13.3 % / Rmerge(I) obs: 2.788 / Mean I/σ(I) obs: 1.13 / CC1/2: 0.575 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4bwz Resolution: 3.7→33.64 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0.48 / Phase error: 36.34 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.7→33.64 Å
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Refine LS restraints |
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LS refinement shell |
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