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Open data
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Basic information
Entry | Database: PDB / ID: 3c8o | ||||||
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Title | The Crystal Structure of RraA from PAO1 | ||||||
![]() | Regulator of ribonuclease activity A | ||||||
![]() | HYDROLASE REGULATOR / RraA / PAO1 / RNase E regulater | ||||||
Function / homology | ![]() 4-hydroxy-4-methyl-2-oxoglutarate aldolase / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / ribonuclease inhibitor activity / regulation of RNA metabolic process / oxaloacetate decarboxylase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Luo, M. / Niu, S. / Yin, Y. / Huang, A. / Wang, D. | ||||||
![]() | ![]() Title: The Crystal Structure of RraA from PAO1 Authors: Luo, M. / Niu, S. / Yin, Y. / Huang, A. / Wang, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.2 KB | Display | ![]() |
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PDB format | ![]() | 63.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.6 KB | Display | ![]() |
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Full document | ![]() | 500.9 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1q5xS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17421.838 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 202 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PGE / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM Tris-HCl pH 8.5, 30% (v/v) PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 13, 2007 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 39611 / Num. obs: 39040 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 8 % / Biso Wilson estimate: 35.735 Å2 / Rmerge(I) obs: 0.0653 / Rsym value: 0.0632 / Net I/σ(I): 11.2 |
Reflection shell | Highest resolution: 1.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 8 / Num. unique all: 39040 / Rsym value: 0.45 / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Q5X Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.621 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.134 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.542 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 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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