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Yorodumi- PDB-5v74: Structure of the intact Haliangium ochraceum microcompartment shell -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v74 | ||||||
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Title | Structure of the intact Haliangium ochraceum microcompartment shell | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / BACTERIAL MICROCOMPARTMENTS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haliangium ochraceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51015467477 Å | ||||||
Authors | Sutter, M. / Kerfeld, C.A. | ||||||
Citation | Journal: Science / Year: 2017 Title: Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell. Authors: Markus Sutter / Basil Greber / Clement Aussignargues / Cheryl A Kerfeld / Abstract: Many bacteria contain primitive organelles composed entirely of protein. These bacterial microcompartments share a common architecture of an enzymatic core encapsulated in a selectively permeable ...Many bacteria contain primitive organelles composed entirely of protein. These bacterial microcompartments share a common architecture of an enzymatic core encapsulated in a selectively permeable protein shell; prominent examples include the carboxysome for CO fixation and catabolic microcompartments found in many pathogenic microbes. The shell sequesters enzymatic reactions from the cytosol, analogous to the lipid-based membrane of eukaryotic organelles. Despite available structural information for single building blocks, the principles of shell assembly have remained elusive. We present the crystal structure of an intact shell from , revealing the basic principles of bacterial microcompartment shell construction. Given the conservation among shell proteins of all bacterial microcompartments, these principles apply to functionally diverse organelles and can inform the design and engineering of shells with new functionalities. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v74.cif.gz | 6.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5v74.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5v74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v74_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 5v74_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 5v74_validation.xml.gz | 1021.6 KB | Display | |
Data in CIF | 5v74_validation.cif.gz | 1.4 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/5v74 ftp://data.pdbj.org/pub/pdb/validation_reports/v7/5v74 | HTTPS FTP |
-Related structure data
-Links
-Assembly
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
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