3QZ4 - JenaLib

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Title :   CRYSTAL STRUCTURE OF AN ENDO-1,4-BETA-XYLANASE D (BT_3675) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.74 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   04 Mar 11 (Deposition) - 06 Apr 11 (Release) - 20 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

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

Keywords :   5-Bladed Beta-Propeller Fold, Xylan Degradation, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of An Endo-1, 4-Beta-Xylanase D (Bt_3675) From Bacteroides Thetaiotaomicron Vpi-5482 At 1. 74 A Resolution
To Be Published
PubMed: search

Molecule 1 - ENDO-1,4-BETA-XYLANASE D
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEQUENCE DATABASE RESIDUES 24-333
	Gene	:	BT_3675
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON
	Organism Taxid	:	818

		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 (4, 23)

No.	Name	Count	Type	Full Name
1	EDO	9	Ligand/Ion	1,2-ETHANEDIOL
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
4	UNX	4	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (4, 11)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	UNX	2	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (4, 12)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	UNX	2	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:39 , TRP A:63 , TRP A:100 , GLN A:160 , ILE A:162 , ARG A:311 , HOH A:631 , HOH A:647 , HOH A:703 , HOH A:769 , HOH A:792 , GLY B:62 , TRP B:309	BINDING SITE FOR RESIDUE EPE A 338
02	AC2	SOFTWARE	SER A:153 , PRO A:155 , GLU A:198 , HOH A:419 , HOH A:711 , HOH A:725	BINDING SITE FOR RESIDUE EDO A 339
03	AC3	SOFTWARE	GLY A:35 , PHE A:36 , HOH A:494 , HOH A:601	BINDING SITE FOR RESIDUE EDO A 344
04	AC4	SOFTWARE	SER A:66 , GLU A:87 , MSE A:88 , ASN A:96	BINDING SITE FOR RESIDUE EDO A 345
05	AC5	SOFTWARE	GLY A:62 , TRP A:309 , ASP B:39 , TRP B:63 , TRP B:100 , GLN B:160 , ILE B:162 , ARG B:311 , HOH B:391 , HOH B:412 , HOH B:583 , HOH B:589 , HOH B:764 , HOH B:1004	BINDING SITE FOR RESIDUE EPE B 337
06	AC6	SOFTWARE	SER B:153 , PRO B:155 , GLU B:198 , THR B:201	BINDING SITE FOR RESIDUE EDO B 340
07	AC7	SOFTWARE	TYR B:51 , LYS B:290 , TYR B:292 , HOH B:924	BINDING SITE FOR RESIDUE EDO B 341
08	AC8	SOFTWARE	LYS B:107 , GLY B:173 , LYS B:174 , SER B:175 , LEU B:189 , ASN B:190 , HOH B:744	BINDING SITE FOR RESIDUE EDO B 342
09	AC9	SOFTWARE	TYR B:67 , GLU B:87 , HOH B:484 , HOH B:646 , HOH B:682	BINDING SITE FOR RESIDUE EDO B 343
10	BC1	SOFTWARE	LEU B:76 , LYS B:77 , TYR B:292 , ILE B:315 , HOH B:540 , HOH B:746 , HOH B:888	BINDING SITE FOR RESIDUE EDO B 346

(no "SS Bond" information available for 3QZ4)

Asymmetric Unit

No.	Residues
1	Asn A:30	-	Pro A:31
2	Gly A:141	-	Pro A:142
3	Gly A:255	-	Pro A:256
4	Asn B:30	-	Pro B:31
5	Gly B:141	-	Pro B:142
6	Gly B:255	-	Pro B:256

(no "SAP(SNP)/Variant" information available for 3QZ4)

(no "PROSITE Motif" information available for 3QZ4)

(no "Exon" information available for 3QZ4)

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
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Chain A from PDB  Type:PROTEIN  Length:306
 aligned with Q8A1I6_BACTN | Q8A1I6 from UniProtKB/TrEMBL  Length:333

    Alignment length:306
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327      
         Q8A1I6_BACTN    28 SGNPILPGFHADPEVLYSHQTKRYYIYPTSDGFPGWGGSYFKVFSSKNLKTWKEETVILEMGKNVSWANGNAWAPCIEEKKIDGKYKYFFYYSANPTTNKGKQIGVAVADSPTGPFTDLGKPIITSSPTGRGQQIDVDVFTDPVSGKSYLYWGNGYMAGAELNDDMLSIKEETTVVLTPKGGTLQTYAYREAPYVIYRKGIYYFFWSVDDTGSPNYHVVYGTAQSPLGPIEVAKEPIVLIQNPKEEIYGPAHNSILQVPGKDKWYIVYHRINKNHLNDGPGWHREVCIDRMEFNPDGTIKQVIPTP 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeeee....eeeeeeee..hhhhh..ee..eee......ee....ee.......eeeeeeeeeeeeeee..eeeeeeeeeeee......eeeeeee.......ee...................eeee......eeeee.....eeee........hhhhhee..............eeeeeeee..eeeeeeee........eeeeeee.......eeeeeeeee..hhhhh.eeeeeeeeee......eeeeeeee.hhhh..hhhh.eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qz4 A  28 SGNPILPGFHADPEVLYSHQTKRYYIYPTSDGFPGWGGSYFKVFSSKNLKTWKEETVILEmGKNVSWANGNAWAPCIEEKKIDGKYKYFFYYSANPTTNKGKQIGVAVADSPTGPFTDLGKPIITSSPTGRGQQIDVDVFTDPVSGKSYLYWGNGYmAGAELNDDmLSIKEETTVVLTPKGGTLQTYAYREAPYVIYRKGIYYFFWSVDDTGSPNYHVVYGTAQSPLGPIEVAKEPIVLIQNPKEEIYGPAHNSILQVPGKDKWYIVYHRINKNHLNDGPGWHREVCIDRmEFNPDGTIKQVIPTP 333
                                    37        47        57        67        77        87|       97       107       117       127       137       147       157       167       177      |187     | 197       207       217       227       237       247       257       267       277       287       297       307       317|      327      
                                                                                       88-MSE                                                                                         184-MSE  193-MSE                                                                                                                      318-MSE

Chain B from PDB  Type:PROTEIN  Length:306
 aligned with Q8A1I6_BACTN | Q8A1I6 from UniProtKB/TrEMBL  Length:333

    Alignment length:306
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327      
         Q8A1I6_BACTN    28 SGNPILPGFHADPEVLYSHQTKRYYIYPTSDGFPGWGGSYFKVFSSKNLKTWKEETVILEMGKNVSWANGNAWAPCIEEKKIDGKYKYFFYYSANPTTNKGKQIGVAVADSPTGPFTDLGKPIITSSPTGRGQQIDVDVFTDPVSGKSYLYWGNGYMAGAELNDDMLSIKEETTVVLTPKGGTLQTYAYREAPYVIYRKGIYYFFWSVDDTGSPNYHVVYGTAQSPLGPIEVAKEPIVLIQNPKEEIYGPAHNSILQVPGKDKWYIVYHRINKNHLNDGPGWHREVCIDRMEFNPDGTIKQVIPTP 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Glyco_hydro_43-3qz4B01 B:28-326                                                                                                                                                                                                                                                                            ------- Pfam domains (1)
           Pfam domains (2) Glyco_hydro_43-3qz4B02 B:28-326                                                                                                                                                                                                                                                                            ------- Pfam domains (2)
         Sec.struct. author .........eeeeeeeee....eeeeeeee..hhhhh..ee..eee......ee....ee.......eeeeeeeeeeeeeee..eeeeeeeeeeee......eeeeeee.......ee...................eeee......eeeee.....eeee........hhhhhee..............eeeeeeee..eeeeeeee........eeeeeee.......eeeeeeeee..hhhhh....eeeeeee......eeeeeeee.hhhh..hhhh.eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qz4 B  28 SGNPILPGFHADPEVLYSHQTKRYYIYPTSDGFPGWGGSYFKVFSSKNLKTWKEETVILEmGKNVSWANGNAWAPCIEEKKIDGKYKYFFYYSANPTTNKGKQIGVAVADSPTGPFTDLGKPIITSSPTGRGQQIDVDVFTDPVSGKSYLYWGNGYmAGAELNDDmLSIKEETTVVLTPKGGTLQTYAYREAPYVIYRKGIYYFFWSVDDTGSPNYHVVYGTAQSPLGPIEVAKEPIVLIQNPKEEIYGPAHNSILQVPGKDKWYIVYHRINKNHLNDGPGWHREVCIDRmEFNPDGTIKQVIPTP 333
                                    37        47        57        67        77        87|       97       107       117       127       137       147       157       167       177      |187     | 197       207       217       227       237       247       257       267       277       287       297       307       317|      327      
                                                                                       88-MSE                                                                                         184-MSE  193-MSE                                                                                                                      318-MSE

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 '\|'

(no "SCOP Domain" information available for 3QZ4)

(no "CATH Domain" information available for 3QZ4)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: B_Fructosidase (34)

Family: Glyco_hydro_43 (11)

Bacteroides thetaiotaomicron (3)

1a	Glyco_hydro_43-3qz4B01	B:28-326
1b	Glyco_hydro_43-3qz4B02	B:28-326

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8A1I6_BACTN | Q8A1I6)

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.
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.
	GO:0045493	xylan catabolic process	The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.

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	Cis Peptide Bonds
		Asn A:30 - Pro A:31	[ RasMol ]
		Asn B:30 - Pro B:31	[ RasMol ]
		Gly A:141 - Pro A:142	[ RasMol ]
		Gly A:255 - Pro A:256	[ RasMol ]
		Gly B:141 - Pro B:142	[ RasMol ]
		Gly B:255 - Pro B:256	[ RasMol ]

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Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 23)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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Exons (0, 0)

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