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Yorodumi- PDB-6q7n: Crystal structure of BH32 alkylated with the mechanistic inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q7n | |||||||||
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Title | Crystal structure of BH32 alkylated with the mechanistic inhibitor 2-bromoacetophenone | |||||||||
Components | BH32 | |||||||||
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: 2.02 Å | |||||||||
Authors | Levy, C.W. | |||||||||
Funding support | United Kingdom, 2items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q7n.cif.gz | 179.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q7n.ent.gz | 120 KB | Display | PDB format |
PDBx/mmJSON format | 6q7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q7n_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 6q7n_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 6q7n_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 6q7n_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/6q7n ftp://data.pdbj.org/pub/pdb/validation_reports/q7/6q7n | HTTPS FTP |
-Related structure data
Related structure data | 6q7oC 6q7pC 6q7qC 6q7rC 2uw6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27676.623 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 |
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#2: Chemical | ChemComp-AC0 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.58 % |
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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. Temp details: Cold room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→41.62 Å / Num. obs: 15995 / % possible obs: 97.97 % / Redundancy: 3.4 % / Biso Wilson estimate: 43.68 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Net I/σ(I): 17.83 |
Reflection shell | Resolution: 2.02→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 1586 / CC1/2: 0.84 / Rpim(I) all: 0.37 / % possible all: 98.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UW6 Resolution: 2.02→41.62 Å / SU ML: 0.2325 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.4713
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→41.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 7.27997535064 Å / Origin y: 1.53184445598 Å / Origin z: 14.8505346468 Å
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Refinement TLS group | Selection details: all |