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Yorodumi- PDB-6a2d: Crystal structure of a synthase 2 from santalum album in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a2d | |||||||||
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Title | Crystal structure of a synthase 2 from santalum album in complex with ligand1 | |||||||||
Components | Sesquisabinene B synthase 2 | |||||||||
Keywords | OXIDOREDUCTASE / substrate binding / synthase / inhibitor | |||||||||
Function / homology | Function and homology information diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Santalum album (white sandalwood) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | |||||||||
Authors | Han, X. / Ko, T.P. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T. | |||||||||
Citation | Journal: To be published Title: Crystal structure of a synthase 2 from santalum album Authors: Han, X. / Ko, T.P. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a2d.cif.gz | 243.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a2d.ent.gz | 192.5 KB | Display | PDB format |
PDBx/mmJSON format | 6a2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a2d_validation.pdf.gz | 822.3 KB | Display | wwPDB validaton report |
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Full document | 6a2d_full_validation.pdf.gz | 838.7 KB | Display | |
Data in XML | 6a2d_validation.xml.gz | 47.3 KB | Display | |
Data in CIF | 6a2d_validation.cif.gz | 70.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/6a2d ftp://data.pdbj.org/pub/pdb/validation_reports/a2/6a2d | HTTPS FTP |
-Related structure data
Related structure data | 6a2aC 2ongS 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: 65517.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Santalum album (white sandalwood) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0RCB5 #2: Chemical | #3: Chemical | ChemComp-MG / #4: 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: 2.38 Å3/Da / Density % sol: 48.27 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: AMMONIUM TARTRATE, PEG 3350, MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.96→25 Å / Num. obs: 90982 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Χ2: 1.025 / Net I/σ(I): 8 / Num. measured all: 606547 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ONG Resolution: 1.96→24.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.029 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.22 Å2 / Biso mean: 35.231 Å2 / Biso min: 11.54 Å2
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Refinement step | Cycle: final / Resolution: 1.96→24.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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