[English] 日本語
Yorodumi- PDB-8qvv: Crystal structure of Ompk36 GD at 3500 eV based on analytical abs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qvv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Ompk36 GD at 3500 eV based on analytical absorption corrections | ||||||
Components | OmpK36 | ||||||
Keywords | MEMBRANE PROTEIN / long-wavelength x-ray diffraction | ||||||
Function / homology | Function and homology information porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Duman, R. / Wagner, A. / Beis, K. / Wong, J. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2024 Title: Ray-tracing analytical absorption correction for X-ray crystallography based on tomographic reconstructions. Authors: Lu, Y. / Duman, R. / Beilsten-Edmands, J. / Winter, G. / Basham, M. / Evans, G. / Kamps, J.J.A.G. / Orville, A.M. / Kwong, H.S. / Beis, K. / Armour, W. / Wagner, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8qvv.cif.gz | 211.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8qvv.ent.gz | 169.4 KB | Display | PDB format |
PDBx/mmJSON format | 8qvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qvv_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8qvv_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8qvv_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 8qvv_validation.cif.gz | 52.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/8qvv ftp://data.pdbj.org/pub/pdb/validation_reports/qv/8qvv | HTTPS FTP |
-Related structure data
Related structure data | 8quqC 8qurC 8quuC 8quvC 8quzC 8qvbC 8qvsC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38231.062 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompK36, ompC_2, DDJ63_09115, NCTC13443_05288 / Production host: Escherichia coli (E. coli) / References: UniProt: D6QLY1 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.55 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M Lithium sulfate, 0.1M sodium citrate pH 5.6 and 12% PEG4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.54 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 3.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→107.43 Å / Num. obs: 60659 / % possible obs: 98.85 % / Redundancy: 11 % / CC1/2: 0.997 / Net I/σ(I): 21.37 |
Reflection shell | Resolution: 2.34→2.424 Å / Num. unique obs: 5633 / CC1/2: 0.874 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→107.43 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.965 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.212 / 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: 39.852 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.34→107.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|