+Open data
-Basic information
Entry | Database: PDB / ID: 6l1n | ||||||
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Title | Substrate bound BacF structure from Bacillus subtillis | ||||||
Components | Aminotransferase | ||||||
Keywords | TRANSFERASE / Aminotransferase / PLP dependent enzyme | ||||||
Function / homology | Function and homology information Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / antibiotic biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Balasubramanian, G. / Deshmukh, A.A. | ||||||
Funding support | India, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Structural insights into the catalytic mechanism of Bacillus subtilis BacF. Authors: Deshmukh, A. / Gopal, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l1n.cif.gz | 165.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l1n.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 6l1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l1n_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6l1n_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6l1n_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 6l1n_validation.cif.gz | 44.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/6l1n ftp://data.pdbj.org/pub/pdb/validation_reports/l1/6l1n | HTTPS FTP |
-Related structure data
Related structure data | 6l1lC 6l1oC 2o1bS 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
#1: Protein | Mass: 44752.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_2089 / Production host: Escherichia coli (E. coli) References: UniProt: A0A164UM01, UniProt: P39643*PLUS, Transferases; Transferring nitrogenous groups; Transaminases #2: Chemical | #3: Chemical | #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: 1.76 Å3/Da / Density % sol: 30.21 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 0.1M sodium acetate trihydrate, 0.1M cacodylate trihydrate (pH= 6.5), 30% w/v polyethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.984 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2→77.76 Å / Num. obs: 42411 / % possible obs: 99.99 % / Redundancy: 6.3 % / CC1/2: 0.991 / Net I/σ(I): 15.46 |
Reflection shell | Resolution: 2→2.072 Å / Num. unique obs: 4243 / CC1/2: 0.737 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O1B Resolution: 2→77.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.767 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.191 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.56 Å2 / Biso mean: 23.702 Å2 / Biso min: 8.58 Å2
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Refinement step | Cycle: final / Resolution: 2→77.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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