[English] 日本語
Yorodumi- PDB-6rnd: Liquid Application Method for time-resolved Analyses (LAMA) by se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rnd | ||||||
---|---|---|---|---|---|---|---|
Title | Liquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Xylose Isomerase 15 ms timepoint | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE / Complex / Diffusion / Dynamics | ||||||
Function / homology | Function and homology information xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces rubiginosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Mehrabi, P. / Schulz, E.C. / Miller, R.J.D. | ||||||
Citation | Journal: Nat.Methods / Year: 2019 Title: Liquid application method for time-resolved analyses by serial synchrotron crystallography. Authors: Mehrabi, P. / Schulz, E.C. / Agthe, M. / Horrell, S. / Bourenkov, G. / von Stetten, D. / Leimkohl, J.P. / Schikora, H. / Schneider, T.R. / Pearson, A.R. / Tellkamp, F. / Miller, R.J.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6rnd.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rnd.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 6rnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/6rnd ftp://data.pdbj.org/pub/pdb/validation_reports/rn/6rnd | HTTPS FTP |
---|
-Related structure data
Related structure data | 6qnbC 6qncC 6qndC 6qnhC 6qniC 6qnjC 6rnbC 6rncC 6rnfC 3kbnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 43283.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Sugar | ChemComp-GLC / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.29 % |
---|---|
Crystal grow | Temperature: 293 K / Method: batch mode Details: 35% (w/v) PEG3350, 200 mM lithium sulfate and 10 mM Hepes/NaOH pH 7.5 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.699→68.526 Å / Num. obs: 45700 / % possible obs: 99.99 % / Redundancy: 492.9 % / Net I/σ(I): 5.36 |
Reflection shell | Resolution: 1.699→1.737 Å / Num. unique obs: 4499 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KBN Resolution: 1.7→68.526 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.13
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→68.526 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|