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- PDB-5iky: Apo structure of Obc1, a bifunctional enzyme for quorum sensing-d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5iky | ||||||
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Title | Apo structure of Obc1, a bifunctional enzyme for quorum sensing-dependent oxalogenesis | ||||||
![]() | Oxalate biosynthetic component 1 | ||||||
![]() | HYDROLASE / LYASE / alpha / beta hydrolase | ||||||
Function / homology | : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oh, J. / Rhee, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insights into an Oxalate-producing Serine Hydrolase with an Unusual Oxyanion Hole and Additional Lyase Activity Authors: Oh, J. / 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 | ![]() | 421.4 KB | Display | ![]() |
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PDB format | ![]() | 343 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ikzC ![]() 4nnaS 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 124417.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: DR63_4704 / Production host: ![]() ![]() |
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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: 5.23 Å3/Da / Density % sol: 76.47 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH 7.0, 1M Sodium citrate tribasic / PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 25, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.5→49.19 Å / Num. obs: 88989 / % possible obs: 99.7 % / Redundancy: 9.1 % / Biso Wilson estimate: 57.13 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.141 / Net I/σ(I): 10.2 | |||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NNA Resolution: 2.5→38.767 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.56 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 280.39 Å2 / Biso mean: 77.9219 Å2 / Biso min: 35.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→38.767 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 14.0477 Å / Origin y: -36.6277 Å / Origin z: 27.1305 Å
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Refinement TLS group |
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