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Yorodumi- PDB-5y06: Structural characterization of msmeg_4306 from Mycobacterium smegmatis -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y06 | ||||||
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Title | Structural characterization of msmeg_4306 from Mycobacterium smegmatis | ||||||
Components | msmeg_4306 | ||||||
Keywords | UNKNOWN FUNCTION / coiled coil helix / zinc ribbon / hypothetical / zinc-SAD | ||||||
Function / homology | C4-type zinc ribbon domain / C4-type zinc ribbon domain / C4-type zinc ribbon domain-containing protein Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.606 Å | ||||||
Authors | Kumar, A. / Karthikeyan, S. | ||||||
Funding support | India, 1items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Crystal structure of the MSMEG_4306 gene product from Mycobacterium smegmatis Authors: Kumar, A. / Karthikeyan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y06.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y06.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/5y06 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/5y06 | HTTPS FTP |
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-Related structure data
Related structure data | 5y05SC 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: 29537.975 Da / Num. of mol.: 1 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: MSMEG_4306 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0R095 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-ZN / |
#4: 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: 2.65 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 8000, 5% PEG 2000 MME, 0.1 M Tris-HCl pH 8.5, 0.1 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 7, 2016 / Details: Mirror |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→66.34 Å / Num. obs: 9152 / % possible obs: 98.2 % / Redundancy: 8.4 % / Biso Wilson estimate: 51 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.034 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.59→2.71 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.621 / Num. unique obs: 955 / CC1/2: 0.7 / Rpim(I) all: 0.23 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y05 Resolution: 2.606→66.338 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.606→66.338 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 133.3993 Å / Origin y: 38.516 Å / Origin z: 87.4645 Å
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Refinement TLS group | Selection details: all |