+Open data
-Basic information
Entry | Database: PDB / ID: 7ed1 | ||||||||||||
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Title | Transferase from Mycobacterium tuberculosis | ||||||||||||
Components | 4'-phosphopantetheinyl transferaseHolo-(acyl-carrier-protein) synthase | ||||||||||||
Keywords | TRANSFERASE / phosphopantetheine transferase | ||||||||||||
Function / homology | COENZYME A / : Function and homology information | ||||||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||||||||
Authors | Kim, D.-G. / Lee, B.-J. / Lee, S.J. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: To Be Published Title: Transferase from Mycobacterium tuberculosis Authors: Kim, D.-G. / Lee, B.-J. / Lee, S.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ed1.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ed1.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ed1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/7ed1 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/7ed1 | HTTPS FTP |
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-Related 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: 25048.408 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: ERS451418_02655 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6HXZ9 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M MES, pH 6.5, 0.2 M calcium chloride, 33%(v/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 64434 / % possible obs: 97.2 % / Redundancy: 4.1 % / CC1/2: 0.996 / Net I/σ(I): 16.44 |
Reflection shell | Resolution: 1.65→1.68 Å / Num. unique obs: 3113 / CC1/2: 0.906 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.229 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.62 Å2 / Biso mean: 17.789 Å2 / Biso min: 6.37 Å2
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Refinement step | Cycle: final / Resolution: 1.65→29.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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