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Yorodumi- PDB-3t5b: Crystal structure of N-terminal domain of FACL13 from Mycobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t5b | ||||||
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Title | Crystal structure of N-terminal domain of FACL13 from Mycobacterium tuberculosis | ||||||
Components | PROBABLE CHAIN-FATTY-ACID-CoA LIGASE FADD13 | ||||||
Keywords | LIGASE / Acetyl-CoA synthetase like fold / AMP-binding | ||||||
Function / homology | Function and homology information long-chain-fatty-acid-CoA ligase / long-chain fatty acid-CoA ligase activity / fatty acid biosynthetic process / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 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 | 3t5b.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t5b.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 3t5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/3t5b ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t5b | HTTPS FTP |
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-Related structure data
Related structure data | 3t5aC 3t5cC 3e53S C: citing same article (ref.) S: Starting model for refinement |
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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: 42841.777 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP RESIDUES 1-396) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: fadD13, MT3174, Rv3089 / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O53306, UniProt: P9WQ36*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: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.2M Na-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-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: Dec 12, 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: 2.35→25 Å / Num. obs: 16344 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 28.17 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 9.13 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.09 / Num. unique all: 1606 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+53 / Resolution: 2.35→25 Å / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.35→25 Å
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