+Open data
-Basic information
Entry | Database: PDB / ID: 7dl0 | ||||||
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Title | The mutant E310G/A314Y of 3,5-DAHDHcca complex with NADPH | ||||||
Components | 3,5-diaminohexanoate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / dehydrogenase / complex / NADPH | ||||||
Function / homology | Function and homology information L-erythro-3,5-diaminohexanoate dehydrogenase / L-erythro-3,5-diaminohexanoate dehydrogenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Cloacimonas acidaminovorans | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å | ||||||
Authors | Liu, N. / Wu, L. / Zhu, D.M. / Zhou, J.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Crystal Structures and Catalytic Mechanism of l-erythro-3,5-Diaminohexanoate Dehydrogenase and Rational Engineering for Asymmetric Synthesis of beta-Amino Acids. Authors: Liu, N. / Wu, L. / Feng, J. / Sheng, X. / Li, J. / Chen, X. / Li, J. / Liu, W. / Zhou, J. / Wu, Q. / Zhu, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dl0.cif.gz | 153.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dl0.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 7dl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dl0_validation.pdf.gz | 763.8 KB | Display | wwPDB validaton report |
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Full document | 7dl0_full_validation.pdf.gz | 776 KB | Display | |
Data in XML | 7dl0_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 7dl0_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/7dl0 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/7dl0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39178.043 Da / Num. of mol.: 2 / Mutation: E310G/A314Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cloacimonas acidaminovorans (strain Evry) (bacteria) Gene: kdd, CLOAM1348 / Production host: Escherichia coli DH1 (bacteria) References: UniProt: B0VJ11, L-erythro-3,5-diaminohexanoate dehydrogenase |
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-Non-polymers , 8 types, 220 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NAP / | #8: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.63 Å3/Da / Density % sol: 53.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgSO4, 14% w/v PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. obs: 44317 / % possible obs: 99.2 % / Redundancy: 0.27 % / Biso Wilson estimate: 35.4133354041 Å2 / Rmerge(I) obs: 0.27 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.17→2.21 Å / Rmerge(I) obs: 1.542 / Num. unique obs: 2029 / Rpim(I) all: 0.501 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.17→40.56 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.12 / Stereochemistry target values: ML
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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 max: 131.85 Å2 / Biso mean: 50.394 Å2 / Biso min: 14.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.17→40.56 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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