+Open data
-Basic information
Entry | Database: PDB / ID: 8iqu | ||||||||||||
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Title | Structure of MtbFadD23 with PhU-AMS | ||||||||||||
Components | Fatty-acid-CoA ligase FadD23 | ||||||||||||
Keywords | LIGASE / long-chain-fatty-acid-AMP ligase | ||||||||||||
Function / homology | Function and homology information long-chain-fatty-acid-CoA ligase / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / long-chain fatty acid-CoA ligase activity / lipid biosynthetic process / membrane Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||||||||
Authors | Yan, M.R. / Zhang, W. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2023 Title: Structural basis for the development of potential inhibitors targeting FadD23 from Mycobacterium tuberculosis. Authors: Yan, M. / Ma, M. / Chen, R. / Cao, Y. / Zhang, W. / Liu, X. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iqu.cif.gz | 228.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iqu.ent.gz | 181.2 KB | Display | PDB format |
PDBx/mmJSON format | 8iqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iqu_validation.pdf.gz | 654 KB | Display | wwPDB validaton report |
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Full document | 8iqu_full_validation.pdf.gz | 662 KB | Display | |
Data in XML | 8iqu_validation.xml.gz | 22 KB | Display | |
Data in CIF | 8iqu_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/8iqu ftp://data.pdbj.org/pub/pdb/validation_reports/iq/8iqu | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Mycobacterium tuberculosis (bacteria) Gene: fadD_1, fadD, fadD_2, ERS007657_01090, ERS007661_00211, ERS007663_00248, ERS007665_00157, ERS007670_01303, ERS007679_02742, ERS007681_00438, ERS007703_00976, ERS007720_00031, ERS007722_00970, ...Gene: fadD_1, fadD, fadD_2, ERS007657_01090, ERS007661_00211, ERS007663_00248, ERS007665_00157, ERS007670_01303, ERS007679_02742, ERS007681_00438, ERS007703_00976, ERS007720_00031, ERS007722_00970, ERS027646_00328, ERS027661_00390, SAMEA2683035_00029 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0E8J579, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases, long-chain-fatty-acid-CoA ligase |
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#2: Chemical | ChemComp-649 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.35 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 30 mM Tris (pH 8.5), 140 mM sodium citrate, 60 mM ammonium phosphate monobasic, 15% w/v (+/-)-2-methyl-2,4-pentanediol, and 14% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→50 Å / Num. obs: 22577 / % possible obs: 99.97 % / Redundancy: 10.3 % / CC1/2: 0.997 / Net I/σ(I): 9.21 |
Reflection shell | Resolution: 2.64→2.8 Å / Num. unique obs: 1613 / CC1/2: 0.941 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→48.65 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.52 / Stereochemistry target values: ML
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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: 2.64→48.65 Å
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Refine LS restraints |
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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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