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Yorodumi- PDB-3t5a: Crystal structure of N-terminal domain of FAAL28 G330W mutant fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t5a | ||||||
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Title | Crystal structure of N-terminal domain of FAAL28 G330W mutant from Mycobacterium tuberculosis | ||||||
Components | Long-chain-fatty-acid--AMP ligase FadD28 | ||||||
Keywords | LIGASE / Acetyl-CoA synthetase like fold / AMP-binding | ||||||
Function / homology | Function and homology information long-chain fatty acid adenylyltransferase FadD28 / Dimycocersyl phthiocerol biosynthesis / adenylyltransferase activity / fatty-acyl-CoA synthase activity / response to host immune response / biological process involved in interaction with host / DIM/DIP cell wall layer assembly / lipid biosynthetic process / ligase activity / fatty acid biosynthetic process ...long-chain fatty acid adenylyltransferase FadD28 / Dimycocersyl phthiocerol biosynthesis / adenylyltransferase activity / fatty-acyl-CoA synthase activity / response to host immune response / biological process involved in interaction with host / DIM/DIP cell wall layer assembly / lipid biosynthetic process / ligase activity / fatty acid biosynthetic process / symbiont-mediated suppression of host innate immune response / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Goyal, A. / Sankaranarayanan, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Molecular basis of the functional divergence of fatty acyl-AMP ligase biosynthetic enzymes of Mycobacterium tuberculosis. Authors: Goyal, A. / Verma, P. / Anandhakrishnan, M. / Gokhale, R.S. / Sankaranarayanan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t5a.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t5a.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 3t5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t5a_validation.pdf.gz | 428.6 KB | Display | wwPDB validaton report |
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Full document | 3t5a_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 3t5a_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3t5a_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/3t5a ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t5a | HTTPS FTP |
-Related structure data
Related structure data | 3t5bC 3t5cC 3e53S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52073.285 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP RESIDUES 1-460) / Mutation: G330W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: acoas, fadD28, MT3011, Rv2941 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P96290, UniProt: P9WQ59*PLUS, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 18% PEG 3350, 0.1M Sodium MES, 5% ethylene glycol, 0.15M Lithium sulphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2008 / Details: Osmic mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→25 Å / Num. obs: 25902 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 31.69 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.63 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.03 / Num. unique all: 2564 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3E53 Resolution: 2.05→25 Å / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.05→25 Å
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