+Open data
-Basic information
Entry | Database: PDB / ID: 1d6f | ||||||
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Title | CHALCONE SYNTHASE C164A MUTANT | ||||||
Components | CHALCONE SYNTHASE | ||||||
Keywords | TRANSFERASE / POLYPETIDE SYNTHASE / FLAVONOID BIOSYNTHESIS / MALONYL-COA DECARBOXYLATION / SITE- DIRECTED MUTANT | ||||||
Function / homology | Function and homology information chalcone biosynthetic process / : / chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process Similarity search - Function | ||||||
Biological species | Medicago sativa (alfalfa) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.69 Å | ||||||
Authors | Jez, J.M. / Ferrer, J.L. / Bowman, M.E. / Dixon, R.A. / Noel, J.P. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Dissection of malonyl-coenzyme A decarboxylation from polyketide formation in the reaction mechanism of a plant polyketide synthase. Authors: Jez, J.M. / Ferrer, J.L. / Bowman, M.E. / Dixon, R.A. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d6f.cif.gz | 95.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d6f.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d6f_validation.pdf.gz | 668.4 KB | Display | wwPDB validaton report |
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Full document | 1d6f_full_validation.pdf.gz | 673.1 KB | Display | |
Data in XML | 1d6f_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1d6f_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/1d6f ftp://data.pdbj.org/pub/pdb/validation_reports/d6/1d6f | HTTPS FTP |
-Related 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: 42723.219 Da / Num. of mol.: 1 / Mutation: C164A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago sativa (alfalfa) / Production host: Escherichia coli (E. coli) / References: UniProt: P30074, chalcone synthase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-B3P / |
#4: 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: 2.11 Å3/Da / Density % sol: 41.58 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.2-2.4 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE, 2 MM DITHIOTHREITOL (DTT), pH 6.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→25 Å / Num. all: 88359 / Num. obs: 39526 / % possible obs: 97 % / Redundancy: 2.2 % / Biso Wilson estimate: 17.48 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.69→1.73 Å / Redundancy: 2 % / Rmerge(I) obs: 0.089 / % possible all: 83.2 |
Reflection | *PLUS Num. measured all: 88359 |
Reflection shell | *PLUS % possible obs: 83.2 % |
-Processing
Software |
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Refinement | Resolution: 1.69→24.45 Å / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.69→24.45 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.17 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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