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- PDB-8hz4: The tetrameric structure of biotin carboxylase from Chloroflexus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hz4 | |||||||||
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Title | The tetrameric structure of biotin carboxylase from Chloroflexus aurantiacus in complex with bicarbonate | |||||||||
![]() | (Biotin carboxylase) x 2 | |||||||||
![]() | LIGASE / biotin carboxylase / biotin carboxyl carrier protein / Chloroflexus aurantiacus / Acetyl-CoA carboxylase / 3-hydroxypropionate cycle | |||||||||
Function / homology | ![]() biotin carboxylase / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shen, J. / Wu, W. / Xu, X. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Chloroflexus aurantiacus acetyl-CoA carboxylase evolves fused biotin carboxylase and biotin carboxyl carrier protein to complete carboxylation activity. Authors: Shen, J. / Wu, W. / Wang, K. / Wu, J. / Liu, B. / Li, C. / Gong, Z. / Hong, X. / Fang, H. / Zhang, X. / Xu, X. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 705 KB | Display | ![]() |
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PDB format | ![]() | 587.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.5 KB | Display | ![]() |
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Full document | ![]() | 506.8 KB | Display | |
Data in XML | ![]() | 61.4 KB | Display | |
Data in CIF | ![]() | 83.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hz5C 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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Unit cell |
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Components
#1: Protein | Mass: 51342.344 Da / Num. of mol.: 4 / Fragment: N-terminal BC domain Source method: isolated from a genetically manipulated source Details: Author stated: Chloroflexus aurantiacus Biotin carboxylase (WP_012257262) is a polypeptide containing 596 amino acids, which is composed of an N-terminal BC domain (Met1-Glu452) and C- ...Details: Author stated: Chloroflexus aurantiacus Biotin carboxylase (WP_012257262) is a polypeptide containing 596 amino acids, which is composed of an N-terminal BC domain (Met1-Glu452) and C-terminal biotin carboxyl carrier domain (BCCP, Ala459-Lys596). However, the crystal structure resolved two homodimers in one asymmetric unit. Each monomer contains the intact BC domain (with chain ID A/B/C/D, length 474), but only partial of the BCCP domain (Arg470-Gly487) was resolved in the crystal structure. A long flexible linker between the BC and BCCP domains are invisible due to lack of clear electron density. It is difficult to distinguish the resolved BCCP domain (Arg470-Gly487) belonging to which chain of the BC domain. For accuracy, we assign the chain ID chain E/F/G/H for the resolved BCCP domain (Arg470-Gly487) in the coordinates. Source: (gene. exp.) ![]() ![]() Gene: Caur_1378 / Plasmid: pET-28a / Production host: ![]() ![]() #2: Protein | Mass: 14249.106 Da / Num. of mol.: 4 / Fragment: BCCP-lile domain Source method: isolated from a genetically manipulated source Details: Author stated: In the Genome of Chloroflexus aurantiacus, Biotin carboxylase (WP_012257262) is composed of BC and BCCP domains. In our tetrameric biotin carboxylase structure, BC and BCCP ...Details: Author stated: In the Genome of Chloroflexus aurantiacus, Biotin carboxylase (WP_012257262) is composed of BC and BCCP domains. In our tetrameric biotin carboxylase structure, BC and BCCP domains are separated due to the poor electronic density of the flexible linker between the two domains. This "separation" confuses us to distinguish which two incomplete chains belong to the same chain. So, we have recoded the new chain for BCCP domain which are chain E,F, G, H. Source: (gene. exp.) ![]() ![]() Gene: Caur_1378 / Plasmid: pET28a / Production host: ![]() ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.55 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Bicine pH 9.0, 2% (v/v) 1,4-Dioxane, 10% (w/v) PEG20,000, 5% (w/v) PEG550 PH range: 7.8-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→28.8 Å / Num. obs: 66529 / % possible obs: 99.22 % / Redundancy: 6.7 % / CC1/2: 0.895 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 3.2→3.314 Å / Num. unique obs: 6647 / CC1/2: 0.65 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→28.8 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 59.3023 Å / Origin y: -18.4379 Å / Origin z: 171.3322 Å
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Refinement TLS group | Selection details: all |