[English] 日本語
![](img/lk-miru.gif)
- PDB-1civ: CHLOROPLAST NADP-DEPENDENT MALATE DEHYDROGENASE FROM FLAVERIA BIDENTIS -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1civ | ||||||
---|---|---|---|---|---|---|---|
Title | CHLOROPLAST NADP-DEPENDENT MALATE DEHYDROGENASE FROM FLAVERIA BIDENTIS | ||||||
![]() | NADP-MALATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / CHLOROPLAST / LIGHT ACTIVATED / NADP-DEPENDENT / DEHYDROGENASE | ||||||
Function / homology | ![]() malate dehydrogenase (NADP+) / L-malate dehydrogenase (NADP+) activity / malate metabolic process / chloroplast / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carr, P.D. / Ashton, A.R. / Verger, D. / Ollis, D.L. | ||||||
![]() | ![]() Title: Chloroplast NADP-malate dehydrogenase: structural basis of light-dependent regulation of activity by thiol oxidation and reduction. Authors: Carr, P.D. / Verger, D. / Ashton, A.R. / Ollis, D.L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and preliminary crystallographic studies of chloroplast NADP-dependent malate dehydrogenase from Flaveria bidentis. Authors: MacPherson, K.H. / Ashton, A.R. / Carr, P.D. / Trevanion, S.J. / Verger, D. / Ollis, D.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 88.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 65 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4mdhS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 42097.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DARKENED LEAVES / Source: (natural) ![]() |
---|---|
#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.8 Å3/Da / Density % sol: 74.68 % Description: BOTH SIRAS AND MOLECULAR REPLACEMENT METHODS WERE USED | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 Details: SEE MACPHERSON ET AL. (1998) ACTA CRYST, D54, 654 - 656, pH 7.50 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 7.5 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 20335 / % possible obs: 98.3 % / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Rmerge(I) obs: 0.132 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % possible obs: 98.3 % / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Num. measured all: 38553 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4MDH Resolution: 2.8→15 Å / Data cutoff low absF: 250 / Cross valid method: R-FREE / σ(F): 4
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.78→2.88 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 15 Å / Rfactor obs: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.372 / Rfactor Rwork: 0.264 |