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Yorodumi- PDB-7cxs: Crystal structure of CmnK, a L-Dap formation enzyme in capreomyci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cxs | ||||||
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Title | Crystal structure of CmnK, a L-Dap formation enzyme in capreomycin biosynthesis | ||||||
Components | CmnK | ||||||
Keywords | BIOSYNTHETIC PROTEIN / CmnB / Lyase / capreomycin | ||||||
Function / homology | Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding domain superfamily / nucleotide binding / CmnK Function and homology information | ||||||
Biological species | Saccharothrix mutabilis subsp. capreolus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Chang, C.Y. / Hsu, S.H. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Biochemistry / Year: 2021 Title: Characterization of Enzymes Catalyzing the Formation of the Nonproteinogenic Amino Acid l-Dap in Capreomycin Biosynthesis. Authors: Hsu, S.H. / Zhang, S. / Huang, S.C. / Wu, T.K. / Xu, Z. / 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 | 7cxs.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cxs.ent.gz | 106.2 KB | Display | PDB format |
PDBx/mmJSON format | 7cxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cxs_validation.pdf.gz | 436.8 KB | Display | wwPDB validaton report |
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Full document | 7cxs_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 7cxs_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 7cxs_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/7cxs ftp://data.pdbj.org/pub/pdb/validation_reports/cx/7cxs | HTTPS FTP |
-Related structure data
Related structure data | 7cxuC 7cxvC 4mp3S 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
#1: Protein | Mass: 37209.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria) Gene: cmnK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6YEI2 #2: Water | ChemComp-HOH / | |
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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: 2.27 Å3/Da / Density % sol: 45.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM MgCl2.6H2O, 30% w/v PEG-550, and 100 mM HEPES |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9732 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9732 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→30 Å / Num. obs: 56430 / % possible obs: 98.6 % / Redundancy: 5.9 % / CC1/2: 0.99 / Net I/σ(I): 42.6 |
Reflection shell | Resolution: 1.83→1.9 Å / Num. unique obs: 5363 / CC1/2: 0.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MP3 Resolution: 1.83→29.973 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.827 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 77.42 Å2 / Biso mean: 20.6 Å2 / Biso min: 8.19 Å2
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Refinement step | Cycle: final / Resolution: 1.83→29.973 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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