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Yorodumi- PDB-2hmt: Diamond-shaped octameric ring structure of an RCK domain with NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hmt | ||||||
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Title | Diamond-shaped octameric ring structure of an RCK domain with NADH bound | ||||||
Components | YuaA proteinYuya | ||||||
Keywords | TRANSPORT PROTEIN / RCK / KTN / KTR / KTRA / KTRAB / membrane protein / ion transporter / symporter | ||||||
Function / homology | Function and homology information monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Albright, R.A. / Morais-Cabral, J.H. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: The RCK Domain of the KtrAB K(+) Transporter: Multiple Conformations of an Octameric Ring. Authors: Albright, R.A. / Ibar, J.L. / Kim, C.U. / Gruner, S.M. / Morais-Cabral, J.H. #1: Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: A Mechanism of Regulating Transmembrane Potassium Flux through a Ligand-Mediated Conformational Switch Authors: Roosild, T.P. / Miller, S. / Booth, I.R. / Choe, S. #2: Journal: Nature / Year: 2002 Title: Crystal structure and mechanism of a calcium-gated potassium channel Authors: Jiang, Y. / Lee, A. / Chen, J. / Cadene, M. / Chait, B.T. / MacKinnon, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hmt.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hmt.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 2hmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/2hmt ftp://data.pdbj.org/pub/pdb/validation_reports/hm/2hmt | HTTPS FTP |
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-Related structure data
Related structure data | 2hmsC 2hmuC 2hmvC 2hmwC 1lsuS 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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Details | The biological assembly is an octameric ring generated from the asymmetric unit dimer using these symmetry operators: X, Y, Z and 2-X, Y, 1-Z and 2-X, 1-Y, Z and X, 1-Y, 1-Z |
-Components
#1: Protein | Mass: 16076.447 Da / Num. of mol.: 2 / Fragment: RCK core domain (KTN), residues 1-144 / Mutation: C22V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yuaA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32080 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 3.21 Å3/Da / Density % sol: 61.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 500mM MgCl2, 50mM Tris pH 8.8, 8.5% (w/v) PEG 2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2005 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9764 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 22051 / Num. obs: 21282 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.107 / Χ2: 1.016 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.59 / Num. unique all: 2140 / Χ2: 1.096 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: single domain of PDB entry 1LSU Resolution: 2.2→50 Å / FOM work R set: 0.855 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 44.465 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.987 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 38
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Xplor file |
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