+Open data
-Basic information
Entry | Database: PDB / ID: 7vu2 | ||||||
---|---|---|---|---|---|---|---|
Title | Chitoporin from Serratia marcescens | ||||||
Components | Chitoporin | ||||||
Keywords | MEMBRANE PROTEIN / Outer membrane protein Chitoporin Specific porin | ||||||
Function / homology | Outer membrane porin, bacterial / outer membrane porin, OprD family / Porin domain superfamily / membrane => GO:0016020 / Chitoporin Function and homology information | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Amornloetwattana, R. / Robinson, R.C. / van den Berg, B. / Suginta, W. | ||||||
Funding support | Thailand, 1items
| ||||||
Citation | Journal: To Be Published Title: Chitoporin from Serratia marcescens Authors: Amornloetwattana, R. / Robinson, R.C. / van den Berg, B. / Suginta, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7vu2.cif.gz | 195.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7vu2.ent.gz | 155.1 KB | Display | PDB format |
PDBx/mmJSON format | 7vu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vu2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7vu2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7vu2_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 7vu2_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/7vu2 ftp://data.pdbj.org/pub/pdb/validation_reports/vu/7vu2 | HTTPS FTP |
-Related structure data
Related structure data | 7vu0S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 49004.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiP, AR325_08275, HMI62_06020 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0QBS3 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-MES / | ||||||
#3: Chemical | #4: Chemical | ChemComp-C8E / ( #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.04 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 8000, calcium acetate, MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97886 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97886 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→94.76 Å / Num. obs: 57273 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.993 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.85→1.89 Å / Rmerge(I) obs: 0.101 / Num. unique obs: 57273 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VU0 Resolution: 1.85→62.423 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.61 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.89 Å2 / Biso mean: 26.5562 Å2 / Biso min: 11.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→62.423 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|