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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   BACTERIAL TYPE 3A CELLULOSE-BINDING DOMAIN

Authors :   J. Tormo, R. Lamed, T. A. Steitz

Date :   10 Sep 96 (Deposition) - 26 Sep 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A,B

Keywords :   Cellulose Degradation, Cellulose-Binding Domain, Cellulosome, Scafoldin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Tormo, R. Lamed, A. J. Chirino, E. Morag, E. A. Bayer, Y. Shoham, T. A. Steitz
Crystal Structure Of A Bacterial Family-Iii Cellulose-Binding Domain: A General Mechanism For Attachment To Cellulose.
Embo J. V. 15 5739 1996
PubMed-ID: 8918451
(for further references see the PDB file header)

Molecule 1 - CELLULOSOMAL SCAFFOLDING PROTEIN A
	Atcc	:	SIMILAR TO ATCC 27405
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	CIPB
	Expression System Plasmid	:	PCBD
	Expression System Taxid	:	562
	Expression System Vector Type	:	BACTERIAL
	Fragment	:	CELLULOSE-BINDING DOMAIN
	Gene	:	CIPB
	Organism Scientific	:	CLOSTRIDIUM THERMOCELLUM
	Organism Taxid	:	1515
	Strain	:	YS
	Synonym	:	SCAFOLDIN SUBUNIT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:44 , ASP A:46 , THR A:122 , ASN A:125 , ASP A:126 , HOH A:278	BINDING SITE FOR RESIDUE CA A 156
2	AC2	SOFTWARE	THR B:44 , ASP B:46 , THR B:122 , ASN B:125 , ASP B:126 , HOH B:276	BINDING SITE FOR RESIDUE CA B 156

(no "SS Bond" information available for 1NBC)

(no "Cis Peptide Bond" information available for 1NBC)

(no "SAP(SNP)/Variant" information available for 1NBC)

(no "PROSITE Motif" information available for 1NBC)

(no "Exon" information available for 1NBC)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:155
 aligned with CIPA_CLOTH | Q06851 from UniProtKB/Swiss-Prot  Length:1853

    Alignment length:155
                                   377       387       397       407       417       427       437       447       457       467       477       487       497       507       517     
           CIPA_CLOTH   368 NLKVEFYNSNPSDTTNSINPQFKVTNTGSSAIDLSKLTLRYYYTVDGQKDQTFWCDHAAIIGSNGSYNGITSNVKGTFVKMSSSTNNADTYLEISFTGGTLEPGAHVQIQGRFAKNDWSNYTQSNDYSFKSASQFVEWDQVTAYLNGVLVWGKEP 522
               SCOP domains d1nbca_ A: Cellusomal scaffolding protein A, scaffoldin                                                                                                     SCOP domains
               CATH domains 1nbcA00 A:1-155  [code=2.60.40.710, no name defined]                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeeeeeee.......hhheeeeeee.......eeeeeeeeeee.....eee.hhheeeeeee.........eeeeeee.........eeeeeeeeee..........................eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nbc A   1 NLKVEFYNSNPSDTTNSINPQFKVTNTGSSAIDLSKLTLRYYYTVDGQKDQTFWCDHAAIIGSNGSYNGITSNVKGTFVKMSSSTNNADTYLEISFTGGTLEPGAHVQIQGRFAKNDWSNYTQSNDYSFKSASQFVEWDQVTAYLNGVLVWGKEP 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with CIPA_CLOTH | Q06851 from UniProtKB/Swiss-Prot  Length:1853

    Alignment length:155
                                   377       387       397       407       417       427       437       447       457       467       477       487       497       507       517     
           CIPA_CLOTH   368 NLKVEFYNSNPSDTTNSINPQFKVTNTGSSAIDLSKLTLRYYYTVDGQKDQTFWCDHAAIIGSNGSYNGITSNVKGTFVKMSSSTNNADTYLEISFTGGTLEPGAHVQIQGRFAKNDWSNYTQSNDYSFKSASQFVEWDQVTAYLNGVLVWGKEP 522
               SCOP domains d1nbcb_ B: Cellusomal scaffolding protein A, scaffoldin                                                                                                     SCOP domains
               CATH domains 1nbcB00 B:1-155  [code=2.60.40.710, no name defined]                                                                                                        CATH domains
           Pfam domains (1) ---CBM_3-1nbcB01 B:4-95                                                                        ------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---CBM_3-1nbcB02 B:4-95                                                                        ------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeeeeee.........eeeeeeeee.......hhheeeeeee.......eeeeeeeeeee.....eee.hhheeeeeee.........eeeeeee.........eeeeeeeeee..........................eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nbc B   1 NLKVEFYNSNPSDTTNSINPQFKVTNTGSSAIDLSKLTLRYYYTVDGQKDQTFWCDHAAIIGSNGSYNGITSNVKGTFVKMSSSTNNADTYLEISFTGGTLEPGAHVQIQGRFAKNDWSNYTQSNDYSFKSASQFVEWDQVTAYLNGVLVWGKEP 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f (364)

Superfamily: Carbohydrate-binding domain (66)

Family: Cellulose-binding domain family III (37)

Protein domain: Cellusomal scaffolding protein A, scaffoldin (3)

Clostridium thermocellum [TaxId: 1515] (1)

1a	d1nbca_	A:
1b	d1nbcb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.710, no name defined] (10)

Clostridium thermocellum. Organism_taxid: 1515. Strain: ys. (1)

1a	1nbcA00	A:1-155
1b	1nbcB00	B:1-155

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CBD (21)

Family: CBM_3 (10)

Clostridium thermocellum (strain ATCC 27405 / DSM 1237) (4)

1a	CBM_3-1nbcB01	B:4-95
1b	CBM_3-1nbcB02	B:4-95

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CIPA_CLOTH | Q06851)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0030248	cellulose binding	Interacting selectively and non-covalently with cellulose.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0030245	cellulose catabolic process	The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
	GO:0000272	polysaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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Description

Compounds

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

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