[English] 日本語
Yorodumi- PDB-3tuz: Inward facing conformations of the MetNI methionine ABC transport... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tuz | ||||||
---|---|---|---|---|---|---|---|
Title | Inward facing conformations of the MetNI methionine ABC transporter: CY5 SeMet soak crystal form | ||||||
Components |
| ||||||
Keywords | HYDROLASE/TRANSPORT PROTEIN / ABC-TRANSPORTER / TYPE I ABC TYPE IMPORTER / METHIONINE UPTAKE TRANSPORTER / MEMBRANE PROTEIN / AMINO-ACID TRANSPORT / ATP-BINDING / HYDROLASE / INNER MEMBRANE / HYDROLASE-TRANSPORT PROTEIN complex | ||||||
Function / homology | Function and homology information L-methionine transmembrane transporter activity / ABC-type D-methionine transporter activity / methionine import across plasma membrane / methionine-importing ABC transporter complex / ABC-type methionine transporter / D-methionine transmembrane transport / Gram-negative-bacterium-type cell wall / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / metabolic process ...L-methionine transmembrane transporter activity / ABC-type D-methionine transporter activity / methionine import across plasma membrane / methionine-importing ABC transporter complex / ABC-type methionine transporter / D-methionine transmembrane transport / Gram-negative-bacterium-type cell wall / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / metabolic process / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Johnson, E. / Nguyen, P. / Rees, D.C. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition. Authors: Johnson, E. / Nguyen, P.T. / Yeates, T.O. / Rees, D.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tuz.cif.gz | 431 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tuz.ent.gz | 350.7 KB | Display | PDB format |
PDBx/mmJSON format | 3tuz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/3tuz ftp://data.pdbj.org/pub/pdb/validation_reports/tu/3tuz | HTTPS FTP |
---|
-Related structure data
Related structure data | 3tuiC 3tujC 3dhwS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23269.947 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0198, JW0194, metI, yaeE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: P31547 #2: Protein | Mass: 40610.191 Da / Num. of mol.: 4 / Mutation: E166Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: abc, b0199, JW0195, metN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* References: UniProt: P30750, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances #3: Chemical | ChemComp-MSE / #4: Chemical | ChemComp-ADP / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.06 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% v/v polyethylene glycol 400, 0.1 M tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9801 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 10.3 % / Av σ(I) over netI: 6.4 / Number: 492148 / Rsym value: 0.076 / D res high: 3.195 Å / D res low: 146.772 Å / Num. obs: 47870 / % possible obs: 86.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.195→146.772 Å / Num. all: 47870 / Num. obs: 47870 / % possible obs: 86.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rsym value: 0.076 / Net I/σ(I): 15.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DHW Resolution: 3.4→38.799 Å / Occupancy max: 1 / Occupancy min: 0.56 / FOM work R set: 0.7524 / SU ML: 1.26 / σ(F): 0 / Stereochemistry target values: MLHL
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.005 Å2 / ksol: 0.288 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 213.88 Å2 / Biso mean: 80.7078 Å2 / Biso min: 26.17 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→38.799 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
|