[English] 日本語
Yorodumi- PDB-5uld: Structure and function of the divalent anion/Na+ symporter from V... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uld | ||||||
---|---|---|---|---|---|---|---|
Title | Structure and function of the divalent anion/Na+ symporter from Vibrio cholerae and a humanized variant | ||||||
Components | Transporter, NadC family | ||||||
Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information transmembrane transporter activity / transmembrane transport / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Vibrio cholerae serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.78 Å | ||||||
Authors | Lu, M. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Structure and function of the divalent anion/Na(+) symporter from Vibrio cholerae and a humanized variant. Authors: Nie, R. / Stark, S. / Symersky, J. / Kaplan, R.S. / Lu, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5uld.cif.gz | 334.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5uld.ent.gz | 274.5 KB | Display | PDB format |
PDBx/mmJSON format | 5uld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uld_validation.pdf.gz | 479.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5uld_full_validation.pdf.gz | 530.4 KB | Display | |
Data in XML | 5uld_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 5uld_validation.cif.gz | 83 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/5uld ftp://data.pdbj.org/pub/pdb/validation_reports/ul/5uld | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
|
-Components
#1: Protein | Mass: 47627.773 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0025 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KNE0 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-CIT / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.71 Å3/Da / Density % sol: 73.86 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: PEG, Na+, etc. / Temp details: 293 K |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Nov 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→100 Å / Num. obs: 82226 / % possible obs: 93 % / Redundancy: 27 % / Net I/σ(I): 28 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.78→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.075 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.78→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|