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Open data
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Basic information
Entry | Database: PDB / ID: 4nna | ||||||
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Title | Apo structure of ObcA | ||||||
![]() | OBCA, Oxalate Biosynthetic Component A | ||||||
![]() | LYASE / alpha/beta barrel protein / oxlate biosynthase / Methylation / Seleno-Met labeling | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oh, J.T. / Goo, E. / Hwang, I. / Rhee, S. | ||||||
![]() | ![]() Title: Structural Basis for Bacterial Quorum Sensing-mediated Oxalogenesis. Authors: Oh, J. / Goo, E. / Hwang, I. / Rhee, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.1 KB | Display | ![]() |
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PDB format | ![]() | 93.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.5 KB | Display | ![]() |
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Full document | ![]() | 433.9 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 59853.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: C5AJX5, Lyases; Carbon-carbon lyases; Oxo-acid-lyases |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris pH 8.0, 0.2M magnesium chloride, 20% PEG6000 , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC Quantum Q270r / Detector: CCD | ||||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 40015 / % possible obs: 95.9 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 12.13 | ||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 5.02 / % possible all: 99.75 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.103→38.807 Å
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Refine LS restraints |
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LS refinement shell |
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