+Open data
-Basic information
Entry | Database: PDB / ID: 8h0h | ||||||
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Title | Hypotethical protein from Mycobacterium tuberculsosis | ||||||
Components | Uncharacterized protein Rv1546 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START-like domain superfamily / plasma membrane / Uncharacterized protein Rv1546 Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.74 Å | ||||||
Authors | Kim, D.H. / Na, Y. / Lee, B.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Protein Sci. / Year: 2023 Title: Domain swapping of the C-terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis. Authors: Kim, D.H. / Na, Y. / Chang, H. / Boo, J.H. / Kang, S.M. / Jin, C. / Kang, S.J. / Lee, S.Y. / Lee, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h0h.cif.gz | 145.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h0h.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 8h0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h0h_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 8h0h_full_validation.pdf.gz | 452.2 KB | Display | |
Data in XML | 8h0h_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 8h0h_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/8h0h ftp://data.pdbj.org/pub/pdb/validation_reports/h0/8h0h | HTTPS FTP |
-Related structure data
Related structure data | 8h2dC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15699.864 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv1546, MTCY48.19c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WLU7 #2: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis/Tris Propane/HCl, pH 6.5, 0.2 M sodium fluoride and 20% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→50 Å / Num. obs: 13538 / % possible obs: 96.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 39.57 Å2 / CC1/2: 0.96 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.75→2.8 Å / Num. unique obs: 636 / CC1/2: 0.87 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.74→47.01 Å / SU ML: 0.3755 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.5465 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.74→47.01 Å
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Refine LS restraints |
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LS refinement shell |
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