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- PDB-9qvp: Crystal structure of the CtaG_H128A variant from Ruminiclostridiu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9qvp | ||||||
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Title | Crystal structure of the CtaG_H128A variant from Ruminiclostridium cellulolyticum (P2(1)2(1)2(1)-medium) | ||||||
![]() | Butirosin biosynthesis protein H N-terminal domain-containing protein | ||||||
![]() | LIGASE / Amide Bond Formation / Antibiotics / Biosynthesis / Carrier proteins / Enzymes / Nonribosomal Peptide Synthetases | ||||||
Function / homology | Butirosin biosynthesis protein H N-terminal domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gude, F. / Bohne, A. / Dell, M. / Franke, J. / Dunbar, K.L. / Groll, M. / Hertweck, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Distal peptide elongation by a protease-like ligase and two distinct carrier proteins Authors: Gude, F. / Bohne, A. / Dell, M. / Franke, J. / Dunbar, K.L. / Groll, M. / Hertweck, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 264 KB | Display | ![]() |
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PDB format | ![]() | 212.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.9 KB | Display | ![]() |
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Full document | ![]() | 430.9 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9quzC ![]() 9qvjC ![]() 9qvkC ![]() 9qvlC ![]() 9qvoC ![]() 9qvqC ![]() 9qvrC ![]() 9qvsC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37124.754 Da / Num. of mol.: 2 / Mutation: H128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Ccel_3254 / Plasmid: pET28A / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, 25% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 35280 / % possible obs: 97.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4535 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.91 Å2 / Biso mean: 38.711 Å2 / Biso min: 24 Å2
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Refinement step | Cycle: final / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | T22: 0.0312 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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