[English] 日本語
![](img/lk-miru.gif)
- PDB-1p4n: Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentap... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1p4n | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentapeptide complex | ||||||
![]() |
| ||||||
![]() | Transferase/Transferase Substrate / ![]() | ||||||
Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Biarrotte-Sorin, S. / Maillard, A. / Delettre, J. / Sougakoff, W. / Arthur, M. / Mayer, C. | ||||||
![]() | ![]() Title: Crystal structures of Weissella viridescens FemX and its complex with UDP-MurNAc-pentapeptide: insights into FemABX family substrates recognition. Authors: Biarrotte-Sorin, S. / Maillard, A.P. / Delettre, J. / Sougakoff, W. / Arthur, M. / Mayer, C. | ||||||
History |
| ||||||
Remark 600 | HETEROGEN The residue FGA is gamma-glutamic acid but does not make classical peptide bond. It makes ...HETEROGEN The residue FGA is gamma-glutamic acid but does not make classical peptide bond. It makes peptide bond on the side chain at the Cgamma. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 96.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 70 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1ne9SC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | ![]() Mass: 38195.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Protein/peptide | Mass: 1150.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() | ||||
#3: Chemical | #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.8 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 2K, NaCl, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 14, 2002 Details: two crystals monochromator between two cylindrical parabolic mirrors |
Radiation | Monochromator: Sagitally focused Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→15.57 Å / Num. obs: 27221 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.073 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 3947 / Rsym value: 0.19 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 102033 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.19 |
-
Processing
Software |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() Starting model: PDB ENTRY 1NE9 Resolution: 1.9→15.57 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1090877 / Data cutoff high rms absF: 1090877 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.1592 Å2 / ksol: 0.39732 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
| |||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→15.57 Å
| |||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| |||||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å |