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- PDB-8hiu: Crystal structure of O-carbamoyltransferase VtdB and the compound... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hiu | ||||||
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Title | Crystal structure of O-carbamoyltransferase VtdB and the compound VtdB with carbamoyladenylate from Streptomyces sp. NO1W98 | ||||||
![]() | Carbamoyltransferase | ||||||
![]() | TRANSFERASE / carboxyl- or carbamoyltransferase activity / catalytic activity / transferase activity / ligase activity / magnesium ion binding / metal ion binding | ||||||
Function / homology | Carbamoyltransferase / Carbamoyltransferase, C-terminal / Carbamoyltransferase, C-terminal domain superfamily / Carbamoyltransferase N-terminus / Carbamoyltransferase C-terminus / biosynthetic process / ATPase, nucleotide binding domain / transferase activity / Carbamoyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rao, D. / Teng, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of O-carbamoyltransferase VtdB and the compound VtdB with carbamoyladenylate from Streptomyces sp. NO1W98 Authors: Rao, D. / Teng, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 240.7 KB | Display | ![]() |
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PDB format | ![]() | 191.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 43.9 KB | Display | |
Data in CIF | ![]() | 60.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 65861.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.37 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 30% w/v PEG 2000, 0.1 M MES pH 6.6 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 247145 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rpim(I) all: 0.045 / Net I/σ(I): 13.67 |
Reflection shell | Resolution: 3→3.05 Å / Num. unique obs: 35766 / Rpim(I) all: 0.164 / Rsym value: 0.406 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AlphaFold 2 Resolution: 2.99→31.049 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.861 / SU B: 0.005 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.344 / ESU R Free: 0.44 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.448 Å2
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Refinement step | Cycle: LAST / Resolution: 2.99→31.049 Å
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LS refinement shell |
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