+Open data
-Basic information
Entry | Database: PDB / ID: 5d6n | ||||||
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Title | Crystal structure of a mycobacterial protein | ||||||
Components | Acyl-CoA synthase | ||||||
Keywords | LIGASE / Mycobacterium smegmatis | ||||||
Function / homology | Function and homology information long-chain-fatty-acid-[acyl-carrier-protein] ligase / long-chain fatty acid [acyl-carrier-protein] ligase activity / lipid biosynthetic process / fatty acid metabolic process / ATP binding Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Li, W.J. / Bi, L.J. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Rep / Year: 2015 Title: Crystal structure of FadD32, an enzyme essential for mycolic acid biosynthesis in mycobacteria. Authors: Li, W. / Gu, S. / Fleming, J. / Bi, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d6n.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d6n.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 5d6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d6n_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 5d6n_full_validation.pdf.gz | 425.2 KB | Display | |
Data in XML | 5d6n_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 5d6n_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/5d6n ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d6n | HTTPS FTP |
-Related structure data
Related structure data | 5d6jC 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: 55442.922 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: fadD32, MSMEG_6393, MSMEI_6225 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R618 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.36 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / Details: 0.1 M magnesium formate, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 19911 / % possible obs: 99.8 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.554 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+53 / Resolution: 2.401→25.675 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.41 / Stereochemistry target values: ML
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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: 2.401→25.675 Å
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Refine LS restraints |
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LS refinement shell |
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