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Yorodumi- PDB-2g2d: Crystal structure of a putative pduO-type ATP:cobalamin adenosylt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g2d | ||||||
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Title | Crystal structure of a putative pduO-type ATP:cobalamin adenosyltransferase from Mycobacterium tuberculosis | ||||||
Components | ATP:cobalamin adenosyltransferase | ||||||
Keywords | TRANSFERASE / helix bundle / trimer / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / porphyrin-containing compound biosynthetic process / cobalamin biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Moon, J.H. / Kaviratne, A. / Yu, M. / Bursey, E.H. / Hung, L.-W. / Lekin, T.P. / Segelke, B.W. / Terwilliger, T.C. / Kim, C.-Y. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative pduO-type ATP:cobalamin adenosyltransferase from Mycobacterium tuberculosis. Authors: Moon, J.H. / Kaviratne, A. / Yu, M. / Bursey, E.H. / Hung, L.-W. / Lekin, T.P. / Segelke, B.W. / Terwilliger, T.C. / Kim, C.-Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g2d.cif.gz | 43.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g2d.ent.gz | 31.6 KB | Display | PDB format |
PDBx/mmJSON format | 2g2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g2d_validation.pdf.gz | 418.5 KB | Display | wwPDB validaton report |
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Full document | 2g2d_full_validation.pdf.gz | 419.7 KB | Display | |
Data in XML | 2g2d_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 2g2d_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/2g2d ftp://data.pdbj.org/pub/pdb/validation_reports/g2/2g2d | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a trimer generated by the operations: z, y, x and y, z, x. |
-Components
#1: Protein | Mass: 20718.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P64803, UniProt: P9WP99*PLUS, corrinoid adenosyltransferase |
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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: 2.28 Å3/Da / Density % sol: 45.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 1.6M Ammonium Sulfate, 10% Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. all: 13272 / Num. obs: 13238 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.1 Å2 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→19.8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 5552242.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.7764 Å2 / ksol: 0.356097 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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