[English] 日本語
Yorodumi- PDB-5htp: Putative sugar kinases from Synechococcus elongatus PCC7942 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5htp | ||||||
---|---|---|---|---|---|---|---|
Title | Putative sugar kinases from Synechococcus elongatus PCC7942 in complex with AMPPNP | ||||||
Components | Probable sugar kinase | ||||||
Keywords | TRANSFERASE / putative sugar kinases / Synechococcus elongatus PCC7942 / AMPPNP / complex | ||||||
Function / homology | D-ribulokinase / D-ribulokinase activity / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATP binding / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / D-ribulose kinase Function and homology information | ||||||
Biological species | Synechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Xie, Y. / Li, M. / Chang, W. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana Authors: Xie, Y. / Li, M. / Chang, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5htp.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5htp.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 5htp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/5htp ftp://data.pdbj.org/pub/pdb/validation_reports/ht/5htp | HTTPS FTP |
---|
-Related structure data
Related structure data | 5htjC 5htnC 5htrC 5htvC 5htxC 5htyC 5hu2C 5huxC 5hv7C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 47307.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / Gene: Synpcc7942_2462 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q31KC7 |
---|---|
#2: Chemical | ChemComp-ANP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.58 % |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 18681 / % possible obs: 98.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.18 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 1.79 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.707 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.27
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→24.707 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|