[English] 日本語
Yorodumi- PDB-3r38: 2.23 Angstrom resolution crystal structure of UDP-N-acetylglucosa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r38 | ||||||
---|---|---|---|---|---|---|---|
Title | 2.23 Angstrom resolution crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) from Listeria monocytogenes EGD-e | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1 | ||||||
Keywords | TRANSFERASE / Biosynthesis and Degradation of Murein Sacculus and Peptidoglycan / Infectious Diseases / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / cell cycle / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: 2.23 Angstrom resolution crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) from Listeria monocytogenes EGD-e Authors: Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3r38.cif.gz | 183.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3r38.ent.gz | 145.6 KB | Display | PDB format |
PDBx/mmJSON format | 3r38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/3r38 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/3r38 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2rl2S S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 48768.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo2526, murA, murA1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic References: UniProt: Q8Y4C4, UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||
---|---|---|---|
#2: Chemical | ChemComp-CL / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.22 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 7.6 mg/mL protein in 10 mM Tris-HCl, 0.25 M sodium chloride, 5 mM BME. Crystallization condition: The Classics II Suite condition A5 (0.1 M HEPES, pH 7.5, 2 M ammonium sulfate). Cryo ...Details: 7.6 mg/mL protein in 10 mM Tris-HCl, 0.25 M sodium chloride, 5 mM BME. Crystallization condition: The Classics II Suite condition A5 (0.1 M HEPES, pH 7.5, 2 M ammonium sulfate). Cryo condition: 1:1 v/v 3.6 M ammonium sulfate : 50 % sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2011 / Details: Be-Lenses/Diamond Laue Mono |
Radiation | Monochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→30 Å / Num. all: 26370 / Num. obs: 26370 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.33 |
Reflection shell | Resolution: 2.23→2.29 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.69 / Num. unique all: 1309 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RL2 Resolution: 2.23→29.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.84 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.984 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→29.11 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.23→2.288 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|