[English] 日本語
![](img/lk-miru.gif)
- PDB-4h2k: Crystal structure of the catalytic domain of succinyl-diaminopime... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4h2k | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the catalytic domain of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae | ||||||
![]() | Succinyl-diaminopimelate desuccinylase | ||||||
![]() | HYDROLASE / DapE / MCSG / PSI-Biology / Structural Genomics / Midwest Center for Structural Genomics / Zinc-dependent hydrolase | ||||||
Function / homology | ![]() succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cobalt ion binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nocek, B. / Jedrzejczak, R. / Makowska-Grzyska, M. / Starus, A. / Holz, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The dimerization domain in DapE enzymes is required for catalysis. Authors: Nocek, B. / Starus, A. / Makowska-Grzyska, M. / Gutierrez, B. / Sanchez, S. / Jedrzejczak, R. / Mack, J.C. / Olsen, K.W. / Joachimiak, A. / Holz, R.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 115.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 87.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 445.1 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4onwC ![]() 4op4C ![]() 3iszS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28891.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P44514, succinyl-diaminopimelate desuccinylase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.19 % |
---|---|
Crystal grow | Temperature: 289 K / pH: 5.5 Details: 0.2 M Ammonium acetate, 25% PEG 3350, 0.1 M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2011 / Details: DOUBLE CRYSTAL |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→40 Å / Num. obs: 42453 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.84→1.88 Å / % possible all: 97.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3ISZ Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.756 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.154 / ESU R Free: 0.151 / 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: 24.43 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.84→1.89 Å / Total num. of bins used: 20
|