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Yorodumi- PDB-5fll: Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fll | ||||||
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Title | Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW) from Bacillus subtilis in complex with a Pimeloyl-adenylate | ||||||
Components | 6-CARBOXYHEXANOATE-COA LIGASE | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information 6-carboxyhexanoate-CoA ligase / 6-carboxyhexanoate-CoA ligase activity / biotin biosynthetic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Moynie, L. / Wang, M. / Campopiano, D.J. / Naismith, J.H. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters. Authors: Wang, M. / Moynie, L. / Harrison, P.J. / Kelly, V. / Piper, A. / Naismith, J.H. / Campopiano, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fll.cif.gz | 215.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fll.ent.gz | 180.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fll_validation.pdf.gz | 937.5 KB | Display | wwPDB validaton report |
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Full document | 5fll_full_validation.pdf.gz | 942.1 KB | Display | |
Data in XML | 5fll_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 5fll_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/5fll ftp://data.pdbj.org/pub/pdb/validation_reports/fl/5fll | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.2996, 0.9473, -0.1135), Vector: |
-Components
#1: Protein | Mass: 29674.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53559, 6-carboxyhexanoate-CoA ligase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 19% PEG 400 0.1 M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX / Wavelength: 1.54178 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Sep 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→50 Å / Num. obs: 28257 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.34→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.9 / % possible all: 94.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→35.35 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.925 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.049 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→35.35 Å
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Refine LS restraints |
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