[English] 日本語
Yorodumi- PDB-3bhs: Nitrosomonas europaea Rh50 and mechanism of conduction by Rhesus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bhs | ||||||
---|---|---|---|---|---|---|---|
Title | Nitrosomonas europaea Rh50 and mechanism of conduction by Rhesus protein family of channels | ||||||
Components | Ammonium transporter family protein Rh50 | ||||||
Keywords | TRANSPORT PROTEIN / Ammonia / Rhesus / Rh50 / Channel / Amt / Nitrosomonas / Rh50 Ammonium transporter family / Rh50 Ammonia Transporter / Membrane Protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Transmembrane | ||||||
Function / homology | Function and homology information ammonium homeostasis / ammonium channel activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Nitrosomonas europaea ATCC 19718 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Gruswitz, F. / Ho, C.-M. / del Rosario, M.C. / Westhoff, C.M. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP) | ||||||
Citation | Journal: To be Published Title: Nitrosomonas europaea Rh50 and mechanism of conduction by Rhesus protein family of channels. Authors: Gruswitz, F. / Ho, C.-M. / del Rosario, M.C. / Westhoff, C.M. / Stroud, R.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3bhs.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3bhs.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bhs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bhs_validation.pdf.gz | 423.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3bhs_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 3bhs_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3bhs_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/3bhs ftp://data.pdbj.org/pub/pdb/validation_reports/bh/3bhs | HTTPS FTP |
-Related structure data
Related structure data | 2ns1S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 42518.465 Da / Num. of mol.: 1 / Fragment: Residues 26-425 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria) Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: Rh50, NE0448 / Plasmid: pET52 3C/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82X47 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.74 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1:1 microliter drop ratio of (Protein in 0.02M HEPES pH 7.4, 0.1M NaCl, 0.04M B-octyl glucoside, 2mM Dithiothreitol) and (100mM HEPES, 25% PEG 400). Cryoprotected with 10% Glycerol, pH 7.0, ...Details: 1:1 microliter drop ratio of (Protein in 0.02M HEPES pH 7.4, 0.1M NaCl, 0.04M B-octyl glucoside, 2mM Dithiothreitol) and (100mM HEPES, 25% PEG 400). Cryoprotected with 10% Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 78 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 29, 2007 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 32561 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.097 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.99→2.07 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3221 / Rsym value: 0.395 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2NS1 Resolution: 1.99→40.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.951 / SU ML: 0.111 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.158 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 27.769 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→40.06 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.99→2.05 Å / Total num. of bins used: 20
|