+Open data
-Basic information
Entry | Database: PDB / ID: 6z1l | |||||||||
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Title | A de novo Enzyme for the Morita-Baylis-Hillman Reaction BH32.12 | |||||||||
Components | BH32.12 protein | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Morita-Baylis-Hillman Reaction / engineered / evolved | |||||||||
Function / homology | PHOSPHATE ION Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | |||||||||
Authors | Levy, C.W. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat.Chem. / Year: 2022 Title: Engineering an efficient and enantioselective enzyme for the Morita-Baylis-Hillman reaction. Authors: Crawshaw, R. / Crossley, A.E. / Johannissen, L. / Burke, A.J. / Hay, S. / Levy, C. / Baker, D. / Lovelock, S.L. / Green, A.P. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z1l.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z1l.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 6z1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/6z1l ftp://data.pdbj.org/pub/pdb/validation_reports/z1/6z1l | HTTPS FTP |
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-Related structure data
Related structure data | 6z1kC 7o1dC 6q7oS 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: 27559.633 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) |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M SPG 9.0 25 % w/v PEG 1500 / 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 6M / Detector: PIXEL / Date: Aug 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→42.71 Å / Num. obs: 16121 / % possible obs: 99.55 % / Redundancy: 9.8 % / Biso Wilson estimate: 65.33 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0806 / Rpim(I) all: 0.02701 / Rrim(I) all: 0.08509 / Net I/σ(I): 10.51 |
Reflection shell | Resolution: 2.29→2.372 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.617 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 1571 / CC1/2: 0.603 / CC star: 0.867 / Rpim(I) all: 0.5474 / % possible all: 98.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q7O Resolution: 2.29→42.71 Å / SU ML: 0.3306 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.9881 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→42.71 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: -20.9491046743 Å / Origin y: 26.477902989 Å / Origin z: -11.0134784038 Å
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Refinement TLS group | Selection details: all |