+Open data
-Basic information
Entry | Database: PDB / ID: 1cml | ||||||
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Title | CHALCONE SYNTHASE FROM ALFALFA COMPLEXED WITH MALONYL-COA | ||||||
Components | PROTEIN (CHALCONE SYNTHASE) | ||||||
Keywords | TRANSFERASE / POLYKETIDE SYNTHASE / CHALCONE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information chalcone biosynthetic process / chalcone synthase activity / chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process Similarity search - Function | ||||||
Biological species | Medicago sativa (alfalfa) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.69 Å | ||||||
Authors | Ferrer, J.-L. / Jez, J. / Bowman, M.E. / Dixon, R. / Noel, J.P. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Authors: Ferrer, J.L. / Jez, J.M. / 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 | 1cml.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cml.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 1cml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/1cml ftp://data.pdbj.org/pub/pdb/validation_reports/cm/1cml | HTTPS FTP |
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-Related structure data
Related structure data | 1bi5SC 1bq6C 1cgkC 1cgzC 1chwC 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: 42723.219 Da / Num. of mol.: 1 / Mutation: C164A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago sativa (alfalfa) / Tissue: 21 DAY OLD ROOT NODULE / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30074, chalcone synthase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-MLC / |
#4: Chemical | ChemComp-PIN / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | APPEARS DECARBOXYL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion | ||||||||||||||||||||
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: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Jul 1, 1998 |
Radiation | Monochromator: NI FILTER / 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→84.52 Å / Num. obs: 39507 / % possible obs: 97.3 % / Redundancy: 2.16 % / Rsym value: 0.026 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.69→1.73 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 7.9 / Rsym value: 0.089 / % possible all: 83.2 |
Reflection | *PLUS Highest resolution: 1.69 Å / Lowest resolution: 84.52 Å / % possible obs: 97.3 % / Redundancy: 2.16 % / Rmerge(I) obs: 0.026 |
Reflection shell | *PLUS Highest resolution: 1.69 Å / Lowest resolution: 1.73 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 7.9 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1BI5 Resolution: 1.69→84.52 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.69→84.52 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.69 Å / Lowest resolution: 84.52 Å / Rfactor obs: 0.177 / Rfactor Rfree: 0.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |