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Yorodumi- PDB-7c7m: The structure of SAM-bound CntL, an aminobutyrate transferase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c7m | ||||||
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Title | The structure of SAM-bound CntL, an aminobutyrate transferase in staphylopine biosysnthesis | ||||||
Components | Staphylopine biosynthesis enzyme CntL | ||||||
Keywords | TRANSFERASE / Metallophore / Biosynthesis / Substrate / Aminobutyrate | ||||||
Function / homology | nicotianamine synthase activity / nicotianamine biosynthetic process / Nicotianamine synthase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYLMETHIONINE / D-histidine (S)-2-aminobutanoyltransferase CntL Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å | ||||||
Authors | Luo, Z. / Luo, S. / Zhou, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Faseb J. / Year: 2021 Title: Structural insights into the ligand recognition and catalysis of the key aminobutanoyltransferase CntL in staphylopine biosynthesis. Authors: Luo, Z. / Luo, S. / Ju, Y. / Ding, P. / Xu, J. / Gu, Q. / Zhou, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c7m.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c7m.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 7c7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c7m_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7c7m_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7c7m_validation.xml.gz | 13 KB | Display | |
Data in CIF | 7c7m_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/7c7m ftp://data.pdbj.org/pub/pdb/validation_reports/c7/7c7m | HTTPS FTP |
-Related 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: 32582.947 Da / Num. of mol.: 1 / Mutation: A119T Source method: isolated from a genetically manipulated source Details: M(INITIATING METHIONINE)GSSHHHHHHSS G(EXPRESSION TAG) Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: fmrO, cntL, DDL17_02690, M1K003_1012 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A391FC11 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SAM / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 2.0 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→48.27 Å / Num. obs: 22386 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.81→1.85 Å / Rmerge(I) obs: 0.56 / Num. unique obs: 1292 / CC1/2: 0.958 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.81→48.27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.726 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 20.593 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→48.27 Å
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Refine LS restraints |
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