[English] 日本語
![](img/lk-miru.gif)
- PDB-4loc: Structure of the carboxyl transferase domain from Rhizobium etli ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4loc | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxamate and biotin | ||||||
![]() | Pyruvate carboxylase | ||||||
![]() | LIGASE / TIM Barrel | ||||||
Function / homology | ![]() pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lietzan, A.D. / St.Maurice, M. | ||||||
![]() | ![]() Title: The role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase. Authors: Lietzan, A.D. / Lin, Y. / St.Maurice, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 912.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 755.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4m6vC ![]() 4jx4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 69963.375 Da / Num. of mol.: 4 Fragment: Carboxyl transferase domain, UNP residues 465-1067 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 7 types, 556 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BTN.gif)
![](data/chem/img/OXM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BTN.gif)
![](data/chem/img/OXM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-BTN / #6: Chemical | ChemComp-OXM / #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.3 % |
---|---|
Crystal grow | Temperature: 298 K / Method: batch crystallization under oil / pH: 6 Details: 14% (w/v) PEG 8000, 110 mM MOPS (pH 6.0), 165 mM Tetramethylammonium chloride, 2% (v/v) glycerol, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2011 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. all: 148360 / Num. obs: 145868 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3.4 / % possible all: 94.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4JX4 Resolution: 2.26→43.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.969 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.934 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→43.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|