[English] 日本語
![](img/lk-miru.gif)
- PDB-2vbf: The holostructure of the branched-chain keto acid decarboxylase (... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2vbf | ||||||
---|---|---|---|---|---|---|---|
Title | The holostructure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis | ||||||
![]() | BRANCHED-CHAIN ALPHA-KETOACID DECARBOXYLASE | ||||||
![]() | LYASE / KDCA / FLAVOPROTEIN / THDP-DEPENDENT ENZYMES / THIAMINE PYROPHOSPHATE | ||||||
Function / homology | ![]() branched-chain-2-oxoacid decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / branched-chain amino acid biosynthetic process / thiamine pyrophosphate binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Berthold, C.L. / Gocke, D. / Wood, M.D. / Leeper, F. / Pohl, M. / Schneider, G. | ||||||
![]() | ![]() Title: Crystal Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) from Lactococcus Lactis Provides Insights Into the Structural Basis for the Chemo- and Enantioselective Carboligation Reaction Authors: Berthold, C.L. / Gocke, D. / Wood, M.D. / Leeper, F. / Pohl, M. / Schneider, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 252.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 200 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 968.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 978.4 KB | Display | |
Data in XML | ![]() | 50.4 KB | Display | |
Data in CIF | ![]() | 76.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vbgC ![]() 1ovmS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
|
-
Components
#1: Protein | Mass: 63406.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CHAIN A AND B CONTAIN THE COMPLETE ENZYME SEQUENCE AND SHORT N-TERMINAL TAGS WITH LINKERS, WHICH ARE BOUND IN ADJACENT DIMERS IN THE CRYSTAL. Source: (gene. exp.) ![]() Plasmid: PET28A / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE PROTEIN CONTAINS A 23 AMINO ACID N-TERMINAL EXTENSION, MGSSHHHHHH | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34.71 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 3, 2007 |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→56.17 Å / Num. obs: 127559 / % possible obs: 92.4 % / Observed criterion σ(I): 6 / Redundancy: 3.8 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / % possible all: 63.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OVM Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.674 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE RESIDUES 182-187 HAVE NOT BEEN MODELED DUE TO LACK OF ELECTRON DENSITY THE FLEXIBLE REGION B 538-547 WAS MODELED AT OCCUPANCY 0.5
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.89 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|