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Yorodumi- PDB-8sni: Hydroxynitrile Lyase from Hevea brasiliensis with Forty Mutations -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sni | ||||||||||||
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Title | Hydroxynitrile Lyase from Hevea brasiliensis with Forty Mutations | ||||||||||||
Components | (S)-hydroxynitrile lyase(S)-hydroxynitrile lyase | ||||||||||||
Keywords | LYASE / Engineered Protein / alpha/beta hydrolase fold / esterase / catalytic promiscuity | ||||||||||||
Function / homology | (S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / Methylesterase/Alpha-hydroxynitrile lyase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / BENZOIC ACID / (S)-hydroxynitrile lyase Function and homology information | ||||||||||||
Biological species | Hevea brasiliensis (rubber tree) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||||||||
Authors | Walsh, M.E. / Greenberg, L.R. / Kazlauskas, R.J. / Pierce, C.T. / Aihara, H. / Evans, R.L. / Shi, K. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: To be published Authors: Walsh, M.E. / Greenberg, L.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sni.cif.gz | 140.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sni.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 8sni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/8sni ftp://data.pdbj.org/pub/pdb/validation_reports/sn/8sni | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32793.594 Da / Num. of mol.: 2 Mutation: I9V, T11G, I12A, I18S, E79H, C81L, L84M, H103L, N104A, S105A, V106F, V118L, L121Y, M122N, F125T, D127N, K129L, Y133F, L146M, K147F, L148F, F150P, T151K, L152F, R154A, E155H, N156K, T159Q, ...Mutation: I9V, T11G, I12A, I18S, E79H, C81L, L84M, H103L, N104A, S105A, V106F, V118L, L121Y, M122N, F125T, D127N, K129L, Y133F, L146M, K147F, L148F, F150P, T151K, L152F, R154A, E155H, N156K, T159Q, T173V, G176S, Q180M, Q208K, I209G, F210I, L211P, K236M, L237A, Q238M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Gene: HNL / Production host: Escherichia coli (E. coli) / References: UniProt: P52704, (S)-hydroxynitrile lyase #2: Chemical | ChemComp-EDO / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.37 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES, pH 7.5, 0.2 M L-Proline, 10 % w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→60.85 Å / Num. obs: 39196 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 36.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.054 / Rrim(I) all: 0.086 / Rsym value: 0.066 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.99→2.04 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2786 / CC1/2: 0.698 / Rpim(I) all: 0.774 / Rrim(I) all: 1.244 / Rsym value: 0.967 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→60.85 Å / SU ML: 0.2717 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0219 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: 38.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→60.85 Å
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Refine LS restraints |
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LS refinement shell |
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