+Open data
-Basic information
Entry | Database: PDB / ID: 1bq6 | ||||||
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Title | CHALCONE SYNTHASE FROM ALFALFA WITH COENZYME A | ||||||
Components | CHALCONE SYNTHASE | ||||||
Keywords | TRANSFERASE / POLYKETIDE SYNTHASE / CHALCONE BIOSYNTHESIS | ||||||
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 / SYNCHROTRON / OTHER / Resolution: 1.56 Å | ||||||
Authors | Ferrer, J.-L. / Bowman, M.E. / Jez, J. / 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 | 1bq6.cif.gz | 176.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bq6.ent.gz | 143.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bq6_validation.pdf.gz | 1020.9 KB | Display | wwPDB validaton report |
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Full document | 1bq6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1bq6_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 1bq6_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/1bq6 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/1bq6 | HTTPS FTP |
-Related structure data
Related structure data | 1bi5SC 1cgkC 1cgzC 1chwC 1cmlC 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: 42656.086 Da / Num. of mol.: 1 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-COA / |
#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: 2.07 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / 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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: PT-COATED MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→35.5 Å / Num. obs: 45366 / % possible obs: 91.5 % / Redundancy: 3.5 % / Rsym value: 0.035 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.58→1.62 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.191 / % possible all: 69.6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1BI5 Resolution: 1.56→10 Å / Num. parameters: 31993 / Num. restraintsaints: 40273 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: THE FIRST STEP OF THE REFINEMENT WAS PERFORMED WITH REFMAC AND ARP. ANISOTROPIC SCALING WAS APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. ANISOTROPIC REFINEMENT ...Details: THE FIRST STEP OF THE REFINEMENT WAS PERFORMED WITH REFMAC AND ARP. ANISOTROPIC SCALING WAS APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.84%
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 16 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3364.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.1654 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |