- PDB-4jso: The X-ray crystal structure of a thermophilic cellobiose binding ... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 4jso
Title
The X-ray crystal structure of a thermophilic cellobiose binding protein bound with laminaripentaose
Components
Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
Keywords
SUGAR BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / THERMOPHILIC PROTEIN / CELLULOSE / CELLOPENTAOSE / LAMINARIBIOSE / LAMINARPENTAOSE BINDING PROTEIN
Function / homology
Function and homology information
peptide transport / peptide transmembrane transporter activity / outer membrane-bounded periplasmic space / metal ion binding Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: tmCBP was concentrated to 20 mg/mL and dialyzed into 10 mM Tris, 40 mM NaCl, 0.5 mM TCEP for crystallization. Laminaripentaose was added to a final concentration of 1 mM prior to ...Details: tmCBP was concentrated to 20 mg/mL and dialyzed into 10 mM Tris, 40 mM NaCl, 0.5 mM TCEP for crystallization. Laminaripentaose was added to a final concentration of 1 mM prior to crystallization trials. Crystals were grown in drops containing 2 uL of the protein solution mixed with 2 uL of 0.2-0.3 M magnesium acetate or calcium acetate, 20-30% (wt/vol) PEG 3350 equilibrated against 900 uL of the same solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi