[English] 日本語
Yorodumi- PDB-4m6v: Structure of the carboxyl transferase domain from Rhizobium etli ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m6v | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate and biocytin | |||||||||
Components | PYRUVATE CARBOXYLASE | |||||||||
Keywords | LIGASE / TIM Barrel | |||||||||
Function / homology | Function and homology information pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Rhizobium etli (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Lietzan, A.D. / St.Maurice, M. | |||||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2014 Title: The role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase. Authors: Lietzan, A.D. / Lin, Y. / St.Maurice, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4m6v.cif.gz | 931.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4m6v.ent.gz | 773.4 KB | Display | PDB format |
PDBx/mmJSON format | 4m6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/4m6v ftp://data.pdbj.org/pub/pdb/validation_reports/m6/4m6v | HTTPS FTP |
---|
-Related structure data
Related structure data | 4locC 4jx4S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 69963.375 Da / Num. of mol.: 4 Fragment: CARBOXYL TRANSFERASE DOMAIN, UNP residues 465-1067 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / Gene: pyc, RHE_CH04002 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)* / References: UniProt: Q2K340, pyruvate carboxylase |
---|
-Non-polymers , 7 types, 387 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PYR / #6: Chemical | ChemComp-BYT / #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.92 % |
---|---|
Crystal grow | Temperature: 298 K / Method: batch crystallization under oil / pH: 6 Details: 11% (w/v) PEG 8000, 100 mM BisTris (pH 6.0), 345 mM Tetramethylammonium chloride, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12706 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12706 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 128300 / Num. obs: 128103 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 5.2 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JX4 Resolution: 2.4→49.66 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 15.37 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.213 / 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: 62.797 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|