+
Open data
-
Basic information
Entry | Database: PDB / ID: 1vbg | ||||||
---|---|---|---|---|---|---|---|
Title | Pyruvate Phosphate Dikinase from Maize | ||||||
![]() | pyruvate,orthophosphate dikinase | ||||||
![]() | TRANSFERASE / Maize / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | ![]() pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / pyruvate metabolic process / photosynthesis / chloroplast / kinase activity / phosphorylation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakanishi, T. / Nakatsu, T. / Matsuoka, M. / Sakata, K. / Kato, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion Authors: Nakanishi, T. / Nakatsu, T. / Matsuoka, M. / Sakata, K. / Kato, H. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Purification, crystallization and preliminary X-ray diffraction studies on pyruvate phosphate dikinase from maize Authors: Nakanishi, T. / Ohki, Y. / Oda, J. / Matsuoka, M. / Sakata, K. / Kato, H. #2: Journal: J.BIOL.CHEM. / Year: 1988 Title: Primary structure of maize pyruvate, orthophosphate dikinase as deduced from cDNA sequence Authors: Matsuoka, M. / Ozeki, Y. / Yamamoto, N. / Hirano, H. / Kano-Murakami, Y. / Tanaka, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 182.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 143 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 473 KB | Display | |
Data in XML | ![]() | 35.8 KB | Display | |
Data in CIF | ![]() | 50.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vbhC ![]() 1dikS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 95294.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-MG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.19 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, magnesium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2002 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→73.29 Å / Num. all: 51097 / Num. obs: 51096 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.65 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1DIK Resolution: 2.3→46.03 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2321429.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.5055 Å2 / ksol: 0.365817 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→46.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|