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- PDB-8hd4: Full-length crystal structure of mycobacterium tuberculosis FadD2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hd4 | ||||||
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Title | Full-length crystal structure of mycobacterium tuberculosis FadD23 in complex with AMPC16 | ||||||
![]() | Long-chain-fatty-acid--AMP ligase FadD23 | ||||||
![]() | BIOSYNTHETIC PROTEIN / fatty-acid-AMP synthetase | ||||||
Function / homology | ![]() long-chain fatty acid adenylase/transferase FadD23 / adenylyltransferase activity / sulfolipid biosynthetic process / Actinobacterium-type cell wall biogenesis / ligase activity / fatty acid biosynthetic process / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yan, M.R. / Liu, X. / Zhang, W. / Rao, Z.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Key Roles of Mycobacterium tuberculosis FadD23 C-terminal Domain in Catalytic Mechanisms. Authors: Yan, M. / Cao, L. / Zhao, L. / Zhou, W. / Liu, X. / Zhang, W. / Rao, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224 KB | Display | ![]() |
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PDB format | ![]() | 179.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 692.1 KB | Display | ![]() |
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Full document | ![]() | 700.5 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hczC ![]() 8hdfC ![]() 3e53S S: Starting model for refinement 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: 65202.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: fadD23, Rv3826 / Production host: ![]() ![]() References: UniProt: P9WQ47, long-chain fatty acid adenylase/transferase FadD23 |
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#2: Chemical | ChemComp-1TF / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.2 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 140 mM sodium citrate tribasic dihydrate, 60 mM magnesium chloride hexahydrate, 30 mM tris hydrochloride pH 8.5, 14% (w/v) polyethylene glycol 3350, and 9% (w/v) polyethylene glycol 4000 |
-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: Jan 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→45.87 Å / Num. obs: 22247 / % possible obs: 99.8 % / Redundancy: 9.895 % / Biso Wilson estimate: 68.607 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.11 / Χ2: 0.878 / Net I/σ(I): 13.7 / Num. measured all: 388631 |
Reflection shell | Resolution: 2.68→2.85 Å / Redundancy: 9.349 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 6305 / CC1/2: 0.915 / Rrim(I) all: 0.454 / % possible all: 99.2 |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→45.87 Å
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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