+Open data
-Basic information
Entry | Database: PDB / ID: 7e2v | ||||||
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Title | Crystal structure of MaDA-3 | ||||||
Components | MaDA-3 | ||||||
Keywords | PLANT PROTEIN / enzyme Diels-Alderase cycloaddition stereoselectivity | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | ||||||
Biological species | Morus alba (white mulberry) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å | ||||||
Authors | Gao, L. / Du, X. / Fan, J. / Lei, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Catal / Year: 2021 Title: Enzymatic control of endo- and exo-stereoselective Diels-Alder reactions with broad substrate scope. Authors: Gao, L. / Zou, Y. / Liu, X. / Yang, J. / Du, X. / Wang, J. / Yu, X. / Fan, J. / Jiang, M. / Li, Y. / Houk, K.N. / Lei, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e2v.cif.gz | 254.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e2v.ent.gz | 162.5 KB | Display | PDB format |
PDBx/mmJSON format | 7e2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/7e2v ftp://data.pdbj.org/pub/pdb/validation_reports/e2/7e2v | HTTPS FTP |
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-Related structure data
Related structure data | 6jqhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.445438994483, -0.838450358181, -0.313982641336), (-0.859304009601, -0.498829168544, 0.112987077548), (-0.251357755555, 0.219477692432, -0.942681717892)Vector: 24. ...NCS oper: (Code: given Matrix: (0.445438994483, -0.838450358181, -0.313982641336), Vector: |
-Components
#1: Protein | Mass: 62387.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Morus alba (white mulberry) / Production host: Trichoplusia ni (cabbage looper) #2: Chemical | #3: Sugar | 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: 2.48 Å3/Da / Density % sol: 50.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 10% 2-propanol, 0.1 M Bicine, pH 8.5, 30% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→43.59 Å / Num. obs: 25940 / % possible obs: 99.27 % / Redundancy: 6.5 % / Biso Wilson estimate: 53.88 Å2 / Rpim(I) all: 0.09 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.95→3 Å / Num. unique obs: 1246 / CC1/2: 0.841 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JQH Resolution: 2.94→43.59 Å / SU ML: 0.4997 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.0523 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: 52.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.94→43.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.15607736955 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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