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Yorodumi- PDB-5d2e: crystal structure of an N-terminal ketoreductase from macrolactin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d2e | ||||||
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Title | crystal structure of an N-terminal ketoreductase from macrolactin assembly line | ||||||
Components | MlnE | ||||||
Keywords | OXIDOREDUCTASE / ketoreductase / B-type | ||||||
Function / homology | Function and homology information phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Bacillus amyloliquefaciens subsp. plantarum | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Keatinge-clay, A.T. / Zeng, J. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of an N-terminal ketoreductase from macrolactin polyketide synthase Authors: Zeng, J. / Keatinge-clay, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d2e.cif.gz | 122.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d2e.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 5d2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/5d2e ftp://data.pdbj.org/pub/pdb/validation_reports/d2/5d2e | HTTPS FTP |
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-Related structure data
Related structure data | 4j1sS S: Starting model for refinement |
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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
#1: Protein | Mass: 59052.355 Da / Num. of mol.: 1 / Fragment: UNP residues 1-522 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens subsp. plantarum (strain DSM 23117 / BGSC 10A6 / FZB42) (bacteria) Strain: DSM 23117 / BGSC 10A6 / FZB42 / Gene: mlnE, RBAM_014370 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A7Z474 |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-PG4 / |
#5: 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: 3.03 Å3/Da / Density % sol: 59.41 % |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG3350, sodium malonate / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. obs: 68897 / % possible obs: 95.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.063 / Net I/av σ(I): 2.14 / Net I/σ(I): 18.85 |
Reflection shell | Resolution: 1.721→1.766 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.14 / % possible all: 76.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J1S Resolution: 1.72→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.444 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.096 / 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: 125.19 Å2 / Biso mean: 39.666 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 1.72→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.721→1.766 Å / Total num. of bins used: 20
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