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Yorodumi- PDB-2hms: Rectangular-shaped octameric ring structure of an RCK domain with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hms | ||||||
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Title | Rectangular-shaped octameric ring structure of an RCK domain with NADH bound | ||||||
Components | YuaA proteinYuya | ||||||
Keywords | MEMBRANE PROTEIN / RCK / KTN / KTR / KTRA / KTRAB / 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: 2.7 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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Remark 295 | NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 7 .. 144 C 7 .. 144 0.245 M 1 B 7 .. 140 D 7 .. 140 0.146 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK: |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hms.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hms.ent.gz | 96.1 KB | Display | PDB format |
PDBx/mmJSON format | 2hms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/2hms ftp://data.pdbj.org/pub/pdb/validation_reports/hm/2hms | HTTPS FTP |
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-Related structure data
Related structure data | 2hmtC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9999, -0.0112, 0.0031), Vector: Details | The biological assembly is an octameric ring generated from the two dimers of the asymmetric unit by applying these symmetry operators: X, Y, Z and 2+Y-X, Y, 1/3-Z | |
-Components
#1: Protein | Mass: 16076.447 Da / Num. of mol.: 4 / 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 | ChemComp-NAI / #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: 3.49 Å3/Da / Density % sol: 64.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 100mM sodium acetate pH 5.2, 2M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 24595 / Num. obs: 24578 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.097 / Χ2: 0.998 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.961 / Num. unique all: 2428 / Χ2: 1.037 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: single domain from PDB entry 1LSU Resolution: 2.7→50 Å / FOM work R set: 0.851 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 51.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.616 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→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: 46
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Xplor file |
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