[English] 日本語
Yorodumi- PDB-5jvn: C3-type pyruvate phosphate dikinase: intermediate state of the ce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jvn | ||||||
---|---|---|---|---|---|---|---|
Title | C3-type pyruvate phosphate dikinase: intermediate state of the central domain in the swiveling mechanism | ||||||
Components | Pyruvate, phosphate dikinase, chloroplasticPyruvic acid | ||||||
Keywords | TRANSFERASE / phosphotransferase / nucleotide binding / conformational transition / swiveling mechanism | ||||||
Function / homology | Function and homology information pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / pyruvate metabolic process / photosynthesis / chloroplast / kinase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Flaveria pringlei (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Minges, A. / Hoeppner, A. / Groth, G. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase. Authors: Minges, A. / Ciupka, D. / Winkler, C. / Hoppner, A. / Gohlke, H. / Groth, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jvn.cif.gz | 347.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jvn.ent.gz | 283.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/5jvn ftp://data.pdbj.org/pub/pdb/validation_reports/jv/5jvn | HTTPS FTP |
---|
-Related structure data
Related structure data | 5jvjC 5jvlSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m35jvn / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 95568.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flaveria pringlei (plant) / Gene: PPDK, PDK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q42736, pyruvate, phosphate dikinase |
---|---|
#2: Chemical | ChemComp-6NQ / |
#3: Chemical | ChemComp-PEP / |
#4: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 68.6 % |
---|---|
Crystal grow | Temperature: 285.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 17 % (w/v) PEG 4000, 15 % (w/v) glycerol, 85 mM HEPES (pH 7.5), 5 % (v/v) isopropanol, 10 mM phosphoenol pyruvate, 2.5 mM magnesium sulfate, 1 mM 2'-Br-dAppNHp |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976252 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2015 / Details: Toroidal mirror | ||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.976252 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.9→49.54 Å / Num. obs: 34537 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 65.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.9 | ||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JVL Resolution: 2.9→49.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.582 / ESU R Free: 0.31 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 191.03 Å2 / Biso mean: 90.5836 Å2 / Biso min: 48.59 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.54 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|