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Yorodumi- PDB-9cly: Crystal structure of the 3-ketoacyl-(acyl-carrier-protein) reduct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9cly | ||||||
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Title | Crystal structure of the 3-ketoacyl-(acyl-carrier-protein) reductase, CylG, from Streptococcus agalactiae 2603V/R | ||||||
Components | CylG protein | ||||||
Keywords | OXIDOREDUCTASE / fatty acid and phospholipid metabolism / NAD(P)-dependent dehydrogenase / CSBID / Center for Structural Biology of Infectious Diseases / Structural Genomics / NAD(P)-binding domain-containing protein( | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae 2603V/R (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal structure of the 3-ketoacyl-(acyl-carrier-protein) reductase, CylG, from Streptococcus agalactiae 2603V/R Authors: Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9cly.cif.gz | 245.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cly.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 9cly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cly_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 9cly_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9cly_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 9cly_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/9cly ftp://data.pdbj.org/pub/pdb/validation_reports/cl/9cly | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
-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: 26635.037 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae 2603V/R (bacteria) Gene: cylG, SAG0664 / Plasmid: p53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q8E0R2 #2: Chemical | #3: Chemical | ChemComp-IMD / | #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: 3.46 Å3/Da / Density % sol: 64.41 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 60% Tacsimate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→50 Å / Num. obs: 39959 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 32.39 Å2 / CC1/2: 0.988 / Net I/σ(I): 21.86 |
Reflection shell | Resolution: 2.16→2.2 Å / Num. unique obs: 1970 / CC1/2: 0.815 / Rpim(I) all: 0.253 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→48.29 Å / SU ML: 0.1857 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.8073 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.16→48.29 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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