+Open data
-Basic information
Entry | Database: PDB / ID: 7c9k | ||||||
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Title | Crystal Structure of E84Q mutant of CntL in complex with SAM | ||||||
Components | D-histidine 2-aminobutanoyltransferase | ||||||
Keywords | TRANSFERASE / Metallophore / Biosynthesis / Substrate / Aminobutyrate | ||||||
Function / homology | D-histidine 2-aminobutanoyltransferase / nicotianamine synthase activity / nicotianamine biosynthetic process / Nicotianamine synthase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYLMETHIONINE / D-histidine 2-aminobutanoyltransferase Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus Mu50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Luo, Z. / 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 | 7c9k.cif.gz | 196.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c9k.ent.gz | 155 KB | Display | PDB format |
PDBx/mmJSON format | 7c9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/7c9k ftp://data.pdbj.org/pub/pdb/validation_reports/c9/7c9k | HTTPS FTP |
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-Related structure data
Related structure data | 7c7mSC 7c9mC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31957.143 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Strain: Mu50 / Gene: cntL, SAV2469 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0H3JXA8, D-histidine 2-aminobutanoyltransferase #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: 2.04 Å3/Da / Density % sol: 39.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.3 M caesium acetate, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.540562 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.540562 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→22.79 Å / Num. obs: 14688 / % possible obs: 99.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.407 / Num. unique obs: 1476 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C7M Resolution: 2.75→22.79 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.866 / SU B: 36.04 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / 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: 42.961 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→22.79 Å
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Refine LS restraints |
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