+Open data
-Basic information
Entry | Database: PDB / ID: 6q7o | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of OE1 | |||||||||
Components | OE1 | |||||||||
Keywords | HYDROLASE / Computationally designed enzyme | |||||||||
Function / homology | Function and homology information N-acylneuraminate-9-phosphatase activity / N-acetylneuraminate biosynthetic process / dephosphorylation / metal ion binding Similarity search - Function | |||||||||
Biological species | Pyrococcus horikoshii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Levy, C.W. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: Nature / Year: 2019 Title: Design and evolution of an enzyme with a non-canonical organocatalytic mechanism. Authors: Burke, A.J. / Lovelock, S.L. / Frese, A. / Crawshaw, R. / Ortmayer, M. / Dunstan, M. / Levy, C. / Green, A.P. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6q7o.cif.gz | 188.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6q7o.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 6q7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q7o_validation.pdf.gz | 422.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6q7o_full_validation.pdf.gz | 422.2 KB | Display | |
Data in XML | 6q7o_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 6q7o_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/6q7o ftp://data.pdbj.org/pub/pdb/validation_reports/q7/6q7o | HTTPS FTP |
-Related structure data
Related structure data | 6q7nC 6q7pC 6q7qC 6q7rC 2uw6S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27689.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0459 / Production host: Escherichia coli (E. coli) / References: UniProt: O58216 |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris pH 8.5, 30 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 2→41.43 Å / Num. obs: 16357 / % possible obs: 99.36 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.05 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.039 / Rrim(I) all: 0.072 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 1603 / CC1/2: 0.94 / Rpim(I) all: 0.36 / % possible all: 99.38 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UW6 Resolution: 2→41.43 Å / SU ML: 0.2602 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.2594
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→41.43 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 6.70627101222 Å / Origin y: 1.37985654173 Å / Origin z: 14.8362512245 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |