+Open data
-Basic information
Entry | Database: PDB / ID: 7csh | ||||||
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Title | AtPrR2 with NADP+ and (+)pinoresinol | ||||||
Components | Pinoresinol reductase 2 | ||||||
Keywords | OXIDOREDUCTASE / AtPrR2 / NADP+ / (+)pinoresinol / PLANT PROTEIN | ||||||
Function / homology | Function and homology information (-)-pinoresinol reductase / lignan biosynthetic process / pinoresinol reductase activity / plasmodesma Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59077503881 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 | 7csh.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7csh.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 7csh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7csh_validation.pdf.gz | 1007 KB | Display | wwPDB validaton report |
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Full document | 7csh_full_validation.pdf.gz | 1011 KB | Display | |
Data in XML | 7csh_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 7csh_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/7csh ftp://data.pdbj.org/pub/pdb/validation_reports/cs/7csh | HTTPS FTP |
-Related structure data
Related structure data | 7cs2C 7cs3C 7cs4C 7cs5C 7cs6C 7cs7C 7cs8C 7cs9C 7csaC 7csbC 7cscC 7csdC 7cseC 7csfC 7csgC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35462.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRR2, PLR2, At4g13660, F18A5.50 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SVP6, (-)-pinoresinol reductase |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-GEC / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.1 M DL malic acid, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Mar 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→39.001 Å / Num. obs: 55657 / % possible obs: 99.7 % / Redundancy: 12.9 % / Biso Wilson estimate: 12.9230290314 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.59→1.65 Å / Rmerge(I) obs: 0.475 / Num. unique obs: 5475 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QYD Resolution: 1.59077503881→39.0005 Å / SU ML: 0.100466840733 / Cross valid method: FREE R-VALUE / σ(F): 1.34366837069 / Phase error: 16.7727272879 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: 17.0389862033 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59077503881→39.0005 Å
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Refine LS restraints |
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LS refinement shell |
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