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Yorodumi- PDB-7xbt: Crystal structure of the adenylation domain of CmnG in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xbt | ||||||
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Title | Crystal structure of the adenylation domain of CmnG in complex with AMP | ||||||
Components | CmnG | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Adenylation | ||||||
Function / homology | Function and homology information Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme ...Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain Similarity search - Domain/homology | ||||||
Biological species | Saccharothrix mutabilis subsp. capreolus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Chen, I.H. / Wang, Y.L. / Chang, C.Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Chembiochem / Year: 2022 Title: Characterization and Structural Determination of CmnG-A, the Adenylation Domain That Activates the Nonproteinogenic Amino Acid Capreomycidine in Capreomycin Biosynthesis. Authors: Chen, I.H. / Cheng, T. / Wang, Y.L. / Huang, S.J. / Hsiao, Y.H. / Lai, Y.T. / Toh, S.I. / Chu, J. / Rudolf, J.D. / Chang, C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xbt.cif.gz | 216.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xbt.ent.gz | 169.2 KB | Display | PDB format |
PDBx/mmJSON format | 7xbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/7xbt ftp://data.pdbj.org/pub/pdb/validation_reports/xb/7xbt | HTTPS FTP |
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-Related structure data
Related structure data | 7xbsSC 7xbuC 7xbvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56242.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria) Gene: cmnG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6YEH8 |
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#2: Chemical | ChemComp-AMP / |
#3: Chemical | ChemComp-MG / |
#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: 2.56 Å3/Da / Density % sol: 52.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG-1000, and 100 mM HEPES, pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→30 Å / Num. obs: 51783 / % possible obs: 99.5 % / Redundancy: 8.1 % / Biso Wilson estimate: 18.34 Å2 / CC1/2: 0.977 / Net I/σ(I): 28.79 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 3.54 / Num. unique obs: 5095 / CC1/2: 0.902 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7XBS Resolution: 1.84→25.18 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.82 Å2 / Biso mean: 27.4625 Å2 / Biso min: 7.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→25.18 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Origin x: -7.9473 Å / Origin y: 22.9506 Å / Origin z: 16.4519 Å
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Refinement TLS group |
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