1DYO	Carbohydrate-Binding Module	date	Feb 03, 2000
title	Xylan-Binding Domain From Cbm 22, Formally X6b Domain
authors	G.J.Davies, S.J.Charnock, H.J.Gilbert, C.M.G.A.Fontes
compound		source
Molecule: Endo-1,4-Beta-Xylanase Y Chain: A, B Fragment: Xylan-Binding Domain Synonym: Cbm 22, X6b Domain Engineered: Yes		Organism_scientific: Clostridium Thermocellum Organism_taxid: 1515 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 61 2 2	R_factor 0.190 R_Free 0.250
crystal cell	length a length b length c angle alpha angle beta angle gamma 89.490 89.490 207.690 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	CA, MSE	enzyme
note	1DYO is a representative structure
related structures	by homologous chain: 1H6Y
Gene Ontology	Chain Function Process Component A, B
Primary reference	The X6 "thermostabilizing" domains of xylanases are carbohydrate-binding modules: structure and biochemistry of the Clostridium thermocellum X6b domain., Charnock SJ, Bolam DN, Turkenburg JP, Gilbert HJ, Ferreira LM, Davies GJ, Fontes CM, Biochemistry. 2000 May 2;39(17):5013-21. PMID:10819965

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (62 Kb) [Save to disk] Biological Unit Coordinates (1dyo.pdb1.gz) 29 Kb Biological Unit Coordinates (1dyo.pdb2.gz) 29 Kb LPC: Ligand-Protein Contacts for 1DYO CSU: Contacts of Structural Units for 1DYO Likely Quarternary Molecular Structure file(s) for 1DYO Retrieve 1DYO in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DYO from S2C, [Save to disk]

View 1DYO in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1DYO

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1DYO, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1dyoa_, region A [Jmol] [rasmolscript] [script source]     - Domain d1dyob_, region B [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1dyo_A] [1dyo] [1dyo_B] SWISS-PROT database: [P51584] Domain organization of [XYNY_CLOTM] by SWISSPFAM

Other resources with information on 1DYO

Community annotation for 1DYO at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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Images from IMB Jena Image Library of Biological Macromolecules.

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