+Open data
-Basic information
Entry | Database: PDB / ID: 6sj4 | ||||||
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Title | Amidohydrolase, AHS with substrate analog | ||||||
Components | Amidohydrolase | ||||||
Keywords | HYDROLASE / Amidohydrolase / AHS with substrate analog | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces sp. Tu 6176 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Naismith, J.H. / Song, H. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: The Biosynthesis of the Benzoxazole in Nataxazole Proceeds via an Unstable Ester and has Synthetic Utility. Authors: Song, H. / Rao, C. / Deng, Z. / Yu, Y. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sj4.cif.gz | 393.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sj4.ent.gz | 318.3 KB | Display | PDB format |
PDBx/mmJSON format | 6sj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sj4_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6sj4_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6sj4_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 6sj4_validation.cif.gz | 55 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/6sj4 ftp://data.pdbj.org/pub/pdb/validation_reports/sj/6sj4 | HTTPS FTP |
-Related structure data
Related structure data | 6siwC 6sixC 6siyC 6sizC 6sj0C 6sj1C 6sj2C 6sj3C 6tm4C 6js0 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56400.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. Tu 6176 (bacteria) / Gene: natAM, CF54_07360 / Production host: Streptomyces albus (bacteria) / References: UniProt: A0A022MQ12 |
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-Non-polymers , 6 types, 335 molecules
#2: Chemical | #3: Chemical | ChemComp-PGE / | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.25 Å3/Da / Density % sol: 45.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M MgCl2, 0.1 M Bis-Tris pH 6.5 and 25% w/v polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→65.08 Å / Num. obs: 86621 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.81→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.087 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4510 / CC1/2: 0.587 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JS0 6js0 Resolution: 1.81→65.08 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.877 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.12 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.74 Å2 / Biso mean: 35.811 Å2 / Biso min: 18.45 Å2
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Refinement step | Cycle: final / Resolution: 1.81→65.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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