[English] 日本語
Yorodumi- PDB-8bp1: Crystal structure of BHMeHis1.0, an engineered enzyme for the Mor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bp1 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of BHMeHis1.0, an engineered enzyme for the Morita-Baylis-Hillman reaction | ||||||||||||||||||
Components | BHMeHis1.0 | ||||||||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / Morita-Baylis-Hillman / non-canonical amino acid / methylhistidine / de novo enzyme | ||||||||||||||||||
Function / homology | ACETATE ION / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||||||||||||||
Authors | Hardy, F.J. | ||||||||||||||||||
Funding support | United Kingdom, European Union, France, 5items
| ||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2024 Title: A non-canonical nucleophile unlocks a new mechanistic pathway in a designed enzyme. Authors: Hutton, A.E. / Foster, J. / Crawshaw, R. / Hardy, F.J. / Johannissen, L.O. / Lister, T.M. / Gerard, E.F. / Birch-Price, Z. / Obexer, R. / Hay, S. / Green, A.P. #1: Journal: Res Sq / Year: 2023 Title: A Non-Canonical Nucleophile Unlocks a New Mechanistic Pathway in a Designed Enzyme Authors: Crossley, A. / Crawshaw, R. / Hardy, F.J. / Johannissen, L. / Lister, T. / Gerard, E. / Birch-Price, Z. / Obexer, R. / Hay, S. / Green, A. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8bp1.cif.gz | 192.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8bp1.ent.gz | 129.3 KB | Display | PDB format |
PDBx/mmJSON format | 8bp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bp1_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8bp1_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 8bp1_validation.xml.gz | 13 KB | Display | |
Data in CIF | 8bp1_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/8bp1 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bp1 | HTTPS FTP |
-Related structure data
Related structure data | 8bp0C 7o1dS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27636.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
---|
-Non-polymers , 5 types, 206 molecules
#2: Chemical | ChemComp-PEG / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.18 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium citrate, 29% w/v PEG 4000, pH 6.5, 0.1 M Magnesium acetate tetrahydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→61.5 Å / Num. obs: 37997 / % possible obs: 99.94 % / Redundancy: 20.2 % / Biso Wilson estimate: 30.53 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.08128 / Rpim(I) all: 0.01838 / Net I/σ(I): 20.45 |
Reflection shell | Resolution: 1.72→1.782 Å / Redundancy: 19 % / Rmerge(I) obs: 1.691 / Num. unique obs: 3733 / CC1/2: 0.709 / CC star: 0.911 / % possible all: 99.71 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7O1D Resolution: 1.72→61.5 Å / SU ML: 0.1634 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.7592 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→61.5 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
|