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- PDB-4jx6: Structure of the carboxyl transferase domain Y628A from Rhizobium... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jx6 | |||||||||
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Title | Structure of the carboxyl transferase domain Y628A from Rhizobium etli pyruvate carboxylase with pyruvate | |||||||||
![]() | Pyruvate carboxylase | |||||||||
![]() | Ligase / transferase / 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: A Substrate-induced Biotin Binding Pocket in the Carboxyltransferase Domain of Pyruvate Carboxylase. Authors: Lietzan, A.D. / 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 | ![]() | 878.4 KB | Display | ![]() |
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PDB format | ![]() | 732.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 506.6 KB | Display | ![]() |
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Full document | ![]() | 541.5 KB | Display | |
Data in XML | ![]() | 80.4 KB | Display | |
Data in CIF | ![]() | 108.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jx4C ![]() 4jx5C ![]() 2qf7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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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: 69871.281 Da / Num. of mol.: 4 / Mutation: Y628A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 71 molecules ![](data/chem/img/PYR.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.07 % |
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Crystal grow | Temperature: 298 K / pH: 6 Details: 11.7% (w/v) PEG 8000, 100 mM BisTris (pH 6.0), 200 mM Tetramethylammonium chloride, 3% (v/v) glycerol, 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: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→50 Å / Num. all: 83991 / Num. obs: 83911 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 2.78→2.83 Å / Redundancy: 7 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.3 / % possible all: 99.6 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: CT+ALLOSTERIC DOMAIN (RESI 471-1067) OF PDB ENTRY 2QF7 Resolution: 2.78→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / SU B: 32.99 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.764 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 72.618 Å2
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Refinement step | Cycle: LAST / Resolution: 2.78→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.775→2.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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