+
Open data
-
Basic information
Entry | Database: PDB / ID: 3upk | ||||||
---|---|---|---|---|---|---|---|
Title | E. cloacae MURA in complex with UNAG | ||||||
![]() | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
![]() | TRANSFERASE / MURA / CLOSE ENZYME STATE / CELL WALL / BIOGENESIS/DEGRADATION / PEPTIDOGLYCAN SYNTHESIS | ||||||
Function / homology | ![]() UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhu, J.-Y. / Yang, Y. / Schonbrunn, E. | ||||||
![]() | ![]() Title: Functional Consequence of Covalent Reaction of Phosphoenolpyruvate with UDP-N-acetylglucosamine 1-Carboxyvinyltransferase (MurA). Authors: Zhu, J.Y. / Yang, Y. / Han, H. / Betzi, S. / Olesen, S.H. / Marsilio, F. / Schonbrunn, E. | ||||||
History |
| ||||||
Remark 999 | IAS67 FORMS AN ISOPEPTIDIC BOND AND IS A RESULT OF POSTTRANSLATIONAL MODIFICATION OF ASN67 |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 105 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 78 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3spbC ![]() 3su9C ![]() 3swaC ![]() 3swdC ![]() 3sweC ![]() 3swgC ![]() 3swiC ![]() 3swqC ![]() 3v4tC ![]() 3v5vC ![]() 1pw2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 44829.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-PGE / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-UD1 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.21 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 MG/ML MURA, 5 mM UNAG, 25 MM HEPES PH 7.5, 50 MM BIS-TRIS PH 5.5, 12.5 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 16, 2010 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 29840 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.081 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.288 / % possible all: 99.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1PW2 Resolution: 2→19.59 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6719638.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4448 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
|