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Yorodumi- PDB-3a9v: Crystal structures and enzymatic mechanisms of a Populus tomentos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a9v | ||||||
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Title | Crystal structures and enzymatic mechanisms of a Populus tomentosa 4-coumarate--CoA ligase | ||||||
Components | 4-coumarate--CoA ligase | ||||||
Keywords | LIGASE / 4-coumate--CoA ligase / 4CL / phenylpropanoid pathway | ||||||
Function / homology | Function and homology information 4-coumarate-CoA ligase / 4-coumarate-CoA ligase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Populus tomentosa (Chinese white poplar) | ||||||
Method | X-RAY DIFFRACTION / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Hu, Y. | ||||||
Citation | Journal: Plant Cell / Year: 2010 Title: Crystal structures of a Populus tomentosa 4-coumarate:CoA ligase shed light on its enzymatic mechanisms Authors: Hu, Y. / Gai, Y. / Yin, L. / Wang, X. / Feng, C. / Feng, L. / Li, D. / Jiang, X.N. / Wang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a9v.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a9v.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 3a9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/3a9v ftp://data.pdbj.org/pub/pdb/validation_reports/a9/3a9v | HTTPS FTP |
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-Related structure data
Related structure data | 3a9uSC 3ni2C 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
#1: Protein | Mass: 58607.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus tomentosa (Chinese white poplar) Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q941M3, 4-coumarate-CoA ligase |
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#2: Chemical | ChemComp-AMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.56 % / Mosaicity: 0.677 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein solution: 20mg/ml of Pt4CL1, 50mM Tris pH 7.5, 10%(v/v) glycerol, 0.1M NaCl, 10mM AMP, 2mM DTT, 1mM EDTA, precipitate solution: 50mM MES pH 6.0, 1.8M ammonium citrate, VAPOR ...Details: Protein solution: 20mg/ml of Pt4CL1, 50mM Tris pH 7.5, 10%(v/v) glycerol, 0.1M NaCl, 10mM AMP, 2mM DTT, 1mM EDTA, precipitate solution: 50mM MES pH 6.0, 1.8M ammonium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 24, 2007 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→114.792 Å / Num. all: 24749 / Num. obs: 24708 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2 / Num. measured all: 13811 / Num. unique all: 3556 / Rsym value: 0.381 / % possible all: 99.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: 3A9U Resolution: 2.5→51.34 Å / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 37.561 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.698 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→51.34 Å
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Refine LS restraints |
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Xplor file |
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