STRUCTURE OF FORM III CRYSTALS OF BOVINE PANCREATIC TRYPSIN INHIBITOR

(trypsin)

Authors:              Wlodawer, A.

Release:                1987-10-16      

Classification:     Proteinase Inhibitor (trypsin)  

Experiment:        X-RAY DIFFRACTION with resolution of 1.70 Å   

Residue Count:  58

Compound:        1 Polymer [ Display Full Polymer Details | Display for All Results ]  

1 Ligand [ Display Full Ligand Details | Display for All Results ] 

Citation:               Structure of form III crystals of bovine pancreatic trypsin inhibitor.

(1987) J.Mol.Biol. 198: 469-480 [ Display Full Abstract | Display for All Results ] 

Molecule of the Month: PDB Pioneers, Trypsin

Search Hit:           Classification: PROTEINASE INHIBITOR (TRYPSIN)

Crystal Structure of Human Salivary Alpha-Amylase Dimer

(amylase)

Authors:              Fisher, S.Z.,  Govindasamy, L.,  Tu, C.K.,  Silverman, D.N.,  Rajaniemi, H.,  McKenna, R.

Release:                2005-10-11      

Classification:     Hydrolase  

Experiment:        X-RAY DIFFRACTION with resolution of 3.00 Å   

Residue Count:  992

Compound:        1 Polymer [ Display Full Polymer Details | Display for All Results ]  

2 Ligands [ Display Full Ligand Details | Display for All Results ] 

Citation:               PubMed ID is not available.

Molecule of the Month: Glucansucrase, Alpha-amylase

Search Hit:           Title: Crystal Structure of Human Salivary Alpha-Amylase Dimer

CRYSTAL STRUCTURE OF AN ACIDIC, NON-MYOTOXIC PHOSPHOLIPASE A2 FROM THE VENOM OF BOTHROPS JARARACUSSU

(lipase)

Authors:              Murakami, M.T.,  Watanabe, L.,  Cintra, A.C.O.,  Arni, R.K.

Release:                2003-09-18      

Classification:     Lipase  

Experiment:        X-RAY DIFFRACTION with resolution of 1.79 Å   

Residue Count:  122

Compound:        1 Polymer [ Display Full Polymer Details | Display for All Results ]  

1 Ligand [ Display Full Ligand Details | Display for All Results ] 

Citation:               Crystal Structure of an Acidic Platelet Aggregation Inhibitor and Hypotensive Phospholipase A(2) in the Monomeric and Dimeric States: Insights Into its Oligomeric State

(2004) Biochem.Biophys.Res.Commun. 323: 24 [ Display Full Abstract | Display for All Results ] 

Search Hit:          

Classification: LIPASE

classification	picture
trypsin
amylase
lipase

Intro to rasmol

RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration ofbiological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 90s.[1]
Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computers. Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. RasMol has become an important educational tool as well as continuing to be an important tool for research in structural biology.
RasMol has a complex version history. Starting with the series of 2.7 versions [2] , RasMol is licensed under a dual license (GPL or custom license RASLIC[3]).
RasMol includes a language (for selecting certain protein chains, or changing colors etc.). Jmol and Sirius has
incorporated the RasMol scripting language into its commands.
Protein Databank (PDB) files can be downloaded for visualization from members of the Worldwide Protein Data 
Bank (wwPDB). These have been uploaded by researchers who have characterized the structure of molecules 
usually by X-ray crystallography, NMR spectroscopy orelectron microscopy.

Intro to pdb

The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database). The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted bybiologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, and RCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.

The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.^[1]

Another learning XML~~~

XML

Introduction to XML.

XML stands for Extensible Markup Language. XML was designed to describe data and focus on what data is. It is a markup language much like HTML.

Description of XML.

XML is a software-and hardware-independent tool for carrying information

Difference between XML and HTML.

XML is not a replacement for HTML. These are some of the differences between them.

	XML	HTML
Goal	XML was designed to transport and store data, with focus on what data is	HTML was designed to display data, with focus on how data looks
Tags	-XML language has no predefined tags - XML allows the author to define his own tags and his own document structure	- The tags used in HTML (and the structure of HTML) are predefined -HTML documents can only use tags defined in the HTML standard (like <p>, <h1>, etc.)
Closing Tag	All XML Elements Must Have a Closing Tag	In HTML, you will often see elements that don't have a closing tag: –<p>This is a paragraph<p>This is another paragraph
Properly nested	In XML, all elements must be properly nested within each other: <b><i>This text is bold and italic</i></b>	In HTML, you might see improperly nested elements: <b><i>This text is bold and italic</b></i>
White-space	With XML, the white-space in a document is not truncated	HTML truncates multiple white-space characters to one single white-space:

Well-formed XML Documents.

Well formed XML documents must have a correct syntax, which are:

·        XML documents must have a root element

·        XML elements must have a closing tag

·        XML tags are case sensitive

·        XML elements must be properly nested

·        XML attribute values must be quoted

As we know, XML documents must contain a root element. This element is "the parent" of all other elements. The elements in an XML document form a document tree. The tree starts at the root and branches to the lowest level of the tree.

For example:

Then form a document tree (one book of the document above):

Last but not least, XML is nothing special. It is just plain text. Software that can handle plain text can also handle XML.

www.w3schools.com/xml/xml_whatis.asp