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- PDB-4m6v: Structure of the carboxyl transferase domain from Rhizobium etli ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4m6v | |||||||||
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Title | Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate and biocytin | |||||||||
![]() | PYRUVATE CARBOXYLASE | |||||||||
![]() | LIGASE / TIM Barrel | |||||||||
Function / homology | ![]() pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lietzan, A.D. / St.Maurice, M. | |||||||||
![]() | ![]() Title: The role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase. Authors: Lietzan, A.D. / Lin, Y. / St.Maurice, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 931.7 KB | Display | ![]() |
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PDB format | ![]() | 773.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4locC ![]() 4jx4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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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.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 387 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/BYT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/BYT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#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 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.92 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: LAST / Resolution: 2.4→49.66 Å
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Refine LS restraints |
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