[English] 日本語
Yorodumi- PDB-5iky: Apo structure of Obc1, a bifunctional enzyme for quorum sensing-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iky | ||||||
---|---|---|---|---|---|---|---|
Title | Apo structure of Obc1, a bifunctional enzyme for quorum sensing-dependent oxalogenesis | ||||||
Components | Oxalate biosynthetic component 1 | ||||||
Keywords | HYDROLASE / LYASE / alpha / beta hydrolase | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Burkholderia thailandensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Oh, J. / Rhee, S. | ||||||
Funding support | Korea, Republic Of, 1items
| ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5iky.cif.gz | 421.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5iky.ent.gz | 343 KB | Display | PDB format |
PDBx/mmJSON format | 5iky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/5iky ftp://data.pdbj.org/pub/pdb/validation_reports/ik/5iky | HTTPS FTP |
---|
-Related structure data
Related structure data | 5ikzC 4nnaS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 124417.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) (bacteria) Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: DR63_4704 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A096YSN3 |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.23 Å3/Da / Density % sol: 76.47 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
---|---|
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 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å | |||||||||||||||
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 |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 14.0477 Å / Origin y: -36.6277 Å / Origin z: 27.1305 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|