[English] 日本語
Yorodumi- PDB-7xbv: Crystal structure of the adenylation domain of CmnG in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xbv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the adenylation domain of CmnG in complex with AMPCPP | ||||||
Components | CmnG | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Adenylation | ||||||
Function / homology | Function and homology information amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharothrix mutabilis subsp. capreolus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Chen, I.H. / Wang, Y.L. / Chang, C.Y. | ||||||
Funding support | Taiwan, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xbv.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xbv.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/7xbv ftp://data.pdbj.org/pub/pdb/validation_reports/xb/7xbv | HTTPS FTP |
---|
-Related structure data
Related structure data | 7xbsC 7xbtC 7xbuSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-APC / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.61 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.8 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 5.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→30 Å / Num. obs: 32099 / % possible obs: 99.3 % / Redundancy: 7.7 % / CC1/2: 0.975 / Net I/σ(I): 30.125 |
Reflection shell | Resolution: 1.94→2.02 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.93 / Num. unique obs: 3003 / CC1/2: 0.885 / % possible all: 94.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7XBU Resolution: 1.94→19.94 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.62 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 70.23 Å2 / Biso mean: 21.558 Å2 / Biso min: 6.83 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→19.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.945→1.995 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|