3AXD - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE TRUNCATED FIBROBACTER SUCCINOGENES 1,3-1,4-BETA-D-GLUCANASE V18Y/W203Y IN APO-FORM

Authors :   J. W. Huang, Y. S. Cheng, T. P. Ko, C. Y. Lin, H. L. Lai, C. C. Chen, Y. Ma, C. H Y. Zheng, J. R. Liu, R. T. Guo

Date :   03 Apr 11 (Deposition) - 15 Feb 12 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.53

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Glucanase, Cellobiose/Cellotetraose, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. W. Huang, Y. S. Cheng, T. P. Ko, C. Y. Lin, H. L. Lai, C. C. Chen, Y. Ma, Y. Zheng, C. H. Huang, P. Zou, J. R. Liu, R. T. Guo
Rational Design To Improve Thermostability And Specific Activity Of The Truncated Fibrobacter Succinogenes 1, 3-1, 4-Beta-D-Glucanase
Appl. Microbiol. Biotechnol. V. 94 111 2012
PubMed-ID: 21959377 | Reference-DOI: 10.1007/S00253-011-3586-7

Molecule 1 - BETA-GLUCANASE
	Chains	:	A, B
	EC Number	:	3.2.1.73
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET 32 XA/LIC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 25-271
	Gene	:	FISUC_2961, FSU_0226
	Mutation	:	YES
	Organism Scientific	:	FIBROBACTER SUCCINOGENES
	Organism Taxid	:	59374
	Strain	:	ATCC 19169, S85
	Synonym	:	1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE, ENDO-BETA-1,3-1,4 GLUCANASE, LICHENASE, MIXED LINKAGE BETA-GLUCANASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	CA	8	Ligand/Ion	CALCIUM ION
2	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:40 , GLU A:56 , GLU A:60 , ASN A:139 , TRP A:141 , PHE A:205 , HOH A:416 , HOH A:749	BINDING SITE FOR RESIDUE TRS A 1001
02	AC2	SOFTWARE	PHE A:152 , GLU A:154 , HOH A:301 , HOH A:302 , HOH A:303	BINDING SITE FOR RESIDUE CA A 3001
03	AC3	SOFTWARE	ASN A:164 , ASN A:189 , GLY A:222 , HOH A:304 , HOH A:305 , HOH A:306	BINDING SITE FOR RESIDUE CA A 3002
04	AC4	SOFTWARE	LYS A:200 , ASP A:202 , HOH A:307 , HOH A:308 , HOH A:309 , HOH A:887 , HOH A:991	BINDING SITE FOR RESIDUE CA A 3003
05	AC5	SOFTWARE	ASP A:185 , HOH A:310 , HOH A:311	BINDING SITE FOR RESIDUE CA A 3004
06	AC6	SOFTWARE	MET A:4 , ASP A:6 , HOH A:654 , HOH A:946 , HOH A:948 , HOH A:989	BINDING SITE FOR RESIDUE CA A 3005
07	AC7	SOFTWARE	ASN A:129 , HOH A:682 , HOH A:873 , HOH A:874 , HOH A:875 , HOH A:876	BINDING SITE FOR RESIDUE CA A 3006
08	AC8	SOFTWARE	VAL B:36 , PHE B:40 , GLU B:56 , GLU B:60 , ASN B:139 , TRP B:141	BINDING SITE FOR RESIDUE TRS B 1002
09	AC9	SOFTWARE	ASN B:164 , ASN B:189 , GLY B:222 , HOH B:312 , HOH B:313 , HOH B:314	BINDING SITE FOR RESIDUE CA B 4002
10	BC1	SOFTWARE	LYS B:200 , ASP B:202 , HOH B:315 , HOH B:316 , HOH B:317 , HOH B:318 , HOH B:862	BINDING SITE FOR RESIDUE CA B 4003

(no "SS Bond" information available for 3AXD)

Asymmetric Unit

No.	Residues
1	Ser A:91	-	Pro A:92
2	Leu A:157	-	Pro A:158
3	Ser B:91	-	Pro B:92
4	Leu B:157	-	Pro B:158

(no "SAP(SNP)/Variant" information available for 3AXD)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH16_1	PS01034	Glycosyl hydrolases family 16 active sites.	GUB_FIBSS	79-89	2	A:56-66 B:56-66

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH16_1	PS01034	Glycosyl hydrolases family 16 active sites.	GUB_FIBSS	79-89	1	A:56-66 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH16_1	PS01034	Glycosyl hydrolases family 16 active sites.	GUB_FIBSS	79-89	1	- B:56-66

(no "Exon" information available for 3AXD)

Asymmetric 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:241
 aligned with GUB_FIBSS | P17989 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:241
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266 
            GUB_FIBSS    27 AKDFSGAELYTLEEVQYGKFEARMKMAAASGTVSSMFLYQNGSEIADGRPWVEVDIEVLGKNPGSFQSNIITGKAGAQKTSEKHHAVSPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVSNLTGTQGLRFNLWSSESAAWVGQFDESKLPLFQFINWVKVYKYTPGQGEGGSDFTLDWTDNFDTFDGSRWGKGDWTFDGNRVDLTDKNIYSRDGMLILALTRKGQESFNGQVPRDD 267
               SCOP domains d3axda_ A: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......eeeeeeee......eeeeeeee.............eeeeeee.....eeeeeeeeee..eee...eeee.........eeeeeee...eeeeee..eeeeeee.hhhhhh....eeeeeeee..hhhhhh..hhhhh.eeeeeeeeeeeee....hhhhh.eeeeeee.........eee.........eee....eeee..eeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------GH16_1     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3axd A   4 MKDFSGAELYTLEEYQYGKFEARMKMAAASGTVSSMFLYQNGSEIADGRPWVEVDIEVLGKSPGSFQSNIITGKAGAQKTSEKHHAVSPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVSNLTGTQGLRFNLWSSESAAWVGQFDESKLPLFQFINWVKVYKYTPGQGEGGSDFTLDWTDNFDTFDGSRWGKGDYTFDGNRVDLTDKNIYSRDGMLILALTRKGQESFNGQVPRDD 244
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with GUB_FIBSS | P17989 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:240
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266
            GUB_FIBSS    27 AKDFSGAELYTLEEVQYGKFEARMKMAAASGTVSSMFLYQNGSEIADGRPWVEVDIEVLGKNPGSFQSNIITGKAGAQKTSEKHHAVSPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVSNLTGTQGLRFNLWSSESAAWVGQFDESKLPLFQFINWVKVYKYTPGQGEGGSDFTLDWTDNFDTFDGSRWGKGDWTFDGNRVDLTDKNIYSRDGMLILALTRKGQESFNGQVPRD 266
               SCOP domains d3axdb_ B: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee......eeeeeeee......eeeeeeee.............eeeeeee.....eeeeeeeeee..eee...eeee.........eeeeeee...eeeeee..eeeeeee.hhhhhh....eeeeeeee..hhhhhh..hhhhh.eeeeeeeeeeeee.-------..eeeeeee.........eee.........eee....eeee..eeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------GH16_1     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3axd B   4 MKDFSGAELYTLEEYQYGKFEARMKMAAASGTVSSMFLYQNGSEIADGRPWVEVDIEVLGKSPGSFQSNIITGKAGAQKTSEKHHAVSPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVSNLTGTQGLRFNLWSSESAAWVGQFDESKLPLFQFINWVKVYKYT-------SDFTLDWTDNFDTFDGSRWGKGDYTFDGNRVDLTDKNIYSRDGMLILALTRKGQESFNGQVPRD 243
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163        |-      |183       193       203       213       223       233       243
                                                                                                                                                                                                  172     180

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Glycosyl hydrolases family 16 (29)

Protein domain: automated matches (7)

Fibrobacter succinogenes [TaxId: 59374] (2)

1a	d3axda_	A:
1b	d3axdb_	B:

(no "CATH Domain" information available for 3AXD)

(no "Pfam Domain" information available for 3AXD)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GUB_FIBSS | P17989)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-glycosyl bond.
	GO:0042972	licheninase activity	Catalysis of the hydrolysis of (1->4)-beta-D-glucosidic linkages in beta-D-glucans containing (1->3) and (1->4) bonds.
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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Asymmetric 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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TRS	[ 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 ]

	Cis Peptide Bonds
		Leu A:157 - Pro A:158	[ RasMol ]
		Leu B:157 - Pro B:158	[ RasMol ]
		Ser A:91 - Pro A:92	[ RasMol ]
		Ser B:91 - Pro B:92	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3axd
		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
	GUB_FIBSS \| P17989
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.2.1.73
		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

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
	GUB_FIBSS \| P17989
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GUB_FIBSS \| P17989	:	1mve 1zm1 2r49 3axe 3h0o 3hr9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File