3F2L - JenaLib

Title :   CRYSTAL STRUCTURE ANALYSIS OF THE K171A MUTATION OF N-TERMINAL TYPE II COHESIN 1 FROM THE CELLULOSOMAL SCAB SUBUNIT OF ACETIVIBRIO CELLULOLYTICUS

Authors :   F. Frolow, A. Freeman, Y. Wine, A. Eppel, M. Shanzer, S. Stempler

Date :   30 Oct 08 (Deposition) - 02 Dec 08 (Release) - 02 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

Keywords :   Point Mutation, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Frolow, A. Freeman, Y. Wine, A. Eppel, M. Shanzer, S. Stempler
Crystal Structure Analysis Of The K171A Mutation Of N-Terminal Type Ii Cohesin 1 From The Cellulosomal Scab Subunit Of Acetivibrio Cellulolyticus
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - CELLULOSOMAL SCAFFOLDIN ADAPTOR PROTEIN B
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A+
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL TYPE II COHESIN 1 FROM THE CELLULOSOMAL SCAB SUBUNIT, UNP RESIDUES 28-199
	Mutation	:	YES
	Organism Scientific	:	ACETIVIBRIO CELLULOLYTICUS
	Organism Taxid	:	35830

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Sites (20, 20)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:55 , VAL A:56 , ALA A:57 , THR A:110 , HOH A:283	BINDING SITE FOR RESIDUE EDO A 176
02	AC2	SOFTWARE	ASP A:73 , PHE A:74 , ASP A:100 , NH4 A:190 , HOH A:422	BINDING SITE FOR RESIDUE EDO A 177
03	AC3	SOFTWARE	PRO A:45 , ASN A:71 , LEU A:121 , HOH A:246	BINDING SITE FOR RESIDUE EDO A 178
04	AC4	SOFTWARE	ASN A:75 , ILE A:140 , ASP A:141 , SER A:158 , VAL A:159 , HOH A:211 , HOH A:275	BINDING SITE FOR RESIDUE EDO A 179
05	AC5	SOFTWARE	TYR A:101 , ALA A:106 , LYS A:119 , HOH A:250 , HOH A:282 , HOH A:370	BINDING SITE FOR RESIDUE EDO A 180
06	AC6	SOFTWARE	ASN A:30 , GLN A:109 , THR A:110 , HOH A:241	BINDING SITE FOR RESIDUE EDO A 181
07	AC7	SOFTWARE	VAL A:51 , THR A:52 , SER A:53 , GLY A:55 , LYS A:117 , HOH A:224 , HOH A:330 , HOH A:353 , HOH A:364	BINDING SITE FOR RESIDUE EDO A 182
08	AC8	SOFTWARE	SER A:5 , THR A:32 , ARG A:77 , VAL A:79 , GLY A:156 , HOH A:240 , HOH A:384	BINDING SITE FOR RESIDUE EDO A 183
09	AC9	SOFTWARE	ASN A:71 , ASP A:73 , LYS A:122 , HOH A:279	BINDING SITE FOR RESIDUE EDO A 184
10	BC1	SOFTWARE	THR A:4 , PHE A:146 , GLY A:150 , HOH A:286 , HOH A:428	BINDING SITE FOR RESIDUE EDO A 185
11	BC2	SOFTWARE	LYS A:13 , THR A:14 , VAL A:164 , HOH A:263	BINDING SITE FOR RESIDUE NH4 A 186
12	BC3	SOFTWARE	THR A:68 , LEU A:121 , NH4 A:188 , HOH A:246	BINDING SITE FOR RESIDUE NH4 A 187
13	BC4	SOFTWARE	LEU A:70 , ASN A:71 , SER A:72 , TYR A:95 , GLU A:108 , NH4 A:187	BINDING SITE FOR RESIDUE NH4 A 188
14	BC5	SOFTWARE	ASP A:73 , ASN A:75 , NH4 A:190 , HOH A:415	BINDING SITE FOR RESIDUE NH4 A 189
15	BC6	SOFTWARE	ASN A:75 , SER A:97 , EDO A:177 , NH4 A:189	BINDING SITE FOR RESIDUE NH4 A 190
16	BC7	SOFTWARE	THR A:52 , TYR A:58 , MET A:63 , HOH A:215 , HOH A:260	BINDING SITE FOR RESIDUE NH4 A 191
17	BC8	SOFTWARE	ASN A:27 , ILE A:28 , NH4 A:193	BINDING SITE FOR RESIDUE NH4 A 192
18	BC9	SOFTWARE	GLY A:111 , NH4 A:192 , HOH A:253	BINDING SITE FOR RESIDUE NH4 A 193
19	CC1	SOFTWARE	SER A:53 , ALA A:66 , HOH A:215 , HOH A:362	BINDING SITE FOR RESIDUE EDO A 194
20	CC2	SOFTWARE	THR A:59 , LYS A:60 , SER A:61	BINDING SITE FOR RESIDUE NO3 A 195

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:171
 aligned with Q7WYN3_9FIRM | Q7WYN3 from UniProtKB/TrEMBL  Length:942

    Alignment length:171
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197 
         Q7WYN3_9FIRM    28 APTSSIEIVLDKTTASVGEIVTASINIKNITNFSGCQLNMKYDPAVLQPVTSSGVAYTKSTMPGAGTILNSDFNLRQVADNDLEKGILNFSKAYVSLDDYRTAAAPEQTGTVAVVKFKVLKEETSSISFEDTTSVPNAIDGTVLFDWNGDRIQSGYSVIQPAVINLDMIKA 198
               SCOP domains d3f2la_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains 3f2lA00 A:2-172  [code=2.60.40.680, no name defined]                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........eeeeeeeee....eeeeeeeee.....eeee........................eeeee.......eeeeeeee.hhhhhhhhh.....eeeeeeeeee.....eeeee............eeeee..........eee..eeehhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f2l A   2 APTSSIEIVLDKTTASVGEIVTASINIKNITNFSGCQLNMKYDPAVLQPVTSSGVAYTKSTMPGAGTILNSDFNLRQVADNDLEKGILNFSKAYVSLDDYRTAAAPEQTGTVAVVKFKVLKEETSSISFEDTTSVPNAIDGTVLFDWNGDRIQSGYSVIQPAVINLDMIAA 172
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q7WYN3_9FIRM | Q7WYN3)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NH4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NO3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln A:161 - Pro A:162	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3f2l
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q7WYN3_9FIRM \| Q7WYN3
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q7WYN3_9FIRM \| Q7WYN3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description