+Open data
-Basic information
Entry | Database: PDB / ID: 7cs3 | ||||||
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Title | IiPLR1 with NADP+ | ||||||
Components | Pinoresinol-lariciresinol reductase | ||||||
Keywords | OXIDOREDUCTASE / IiPLR1 / dimer / NADP+ / PLANT PROTEIN | ||||||
Function / homology | pinoresinol reductase activity / : / Phenylcoumaran benzylic ether reductase-like / NmrA-like domain / NmrA-like family / NAD(P)-binding domain superfamily / nucleotide binding / Chem-NDP / Pinoresinol-lariciresinol reductase Function and homology information | ||||||
Biological species | Isatis tinctoria (woad) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4002184429 Å | ||||||
Authors | Shao, K. / Zhang, P. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structure-based engineering of substrate specificity for pinoresinol-lariciresinol reductases. Authors: Xiao, Y. / Shao, K. / Zhou, J. / Wang, L. / Ma, X. / Wu, D. / Yang, Y. / Chen, J. / Feng, J. / Qiu, S. / Lv, Z. / Zhang, L. / Zhang, P. / Chen, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cs3.cif.gz | 437.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cs3.ent.gz | 294.9 KB | Display | PDB format |
PDBx/mmJSON format | 7cs3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/7cs3 ftp://data.pdbj.org/pub/pdb/validation_reports/cs/7cs3 | HTTPS FTP |
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-Related structure data
Related structure data | 7cs2C 7cs4C 7cs5C 7cs6C 7cs7C 7cs8C 7cs9C 7csaC 7csbC 7cscC 7csdC 7cseC 7csfC 7csgC 7cshC 1qydS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 35662.586 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Isatis tinctoria (woad) / Production host: Escherichia coli (E. coli) / References: UniProt: I6LRS1 #2: Chemical | ChemComp-NDP / #3: Water | ChemComp-HOH / | 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: 3 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.2M sodium citrate tribasic, 0.1 M sodium citrate/citric acid, pH 4.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→37.94 Å / Num. obs: 98862 / % possible obs: 99.7 % / Redundancy: 9 % / Biso Wilson estimate: 37.2871101386 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.755 / Num. unique obs: 8674 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QYD Resolution: 2.4002184429→37.9361000379 Å / SU ML: 0.280783611782 / Cross valid method: FREE R-VALUE / σ(F): 1.33944405093 / Phase error: 26.2902577284 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: 34.1550053724 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4002184429→37.9361000379 Å
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Refine LS restraints |
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LS refinement shell |
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