[English] 日本語
Yorodumi- PDB-5nbg: Structure of the cytoplasmic domain I of OutF in the D. dadantii ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nbg | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the cytoplasmic domain I of OutF in the D. dadantii type II secretion system | ||||||
Components | General secretion pathway protein F | ||||||
Keywords | MEMBRANE PROTEIN / inner membrane protein | ||||||
Function / homology | Function and homology information protein secretion by the type II secretion system / type II protein secretion system complex / protein processing / membrane => GO:0016020 / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Dickeya dadantii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Zhang, H. / Gu, S. | ||||||
Citation | Journal: To Be Published Title: Structure of the first cytoplasmic domain of OutF and assembly of the inner-membrane platform proteins of the D. dadantii type II secretion system Authors: Zhang, H. / Gu, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5nbg.cif.gz | 52 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5nbg.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 5nbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/5nbg ftp://data.pdbj.org/pub/pdb/validation_reports/nb/5nbg | HTTPS FTP |
---|
-Related structure data
Related structure data | 3c1qS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11667.410 Da / Num. of mol.: 2 / Fragment: UNP residues 65-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria) Strain: 3937 / Gene: outF, Dda3937_02417 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SM39 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.86 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 100mM sodium cacodyl ate pH 6.5, 200mM Li2SO4 and 30% PEG-400 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972422 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→41.44 Å / Num. obs: 18300 / % possible obs: 99.15 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.037 / Net I/σ(I): 1.35 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.024 / Num. unique obs: 1764 / CC1/2: 0.668 / Rpim(I) all: 0.016 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C1Q Resolution: 2.15→82.15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.98 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.187 / 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: 51.982 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→82.15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|