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(-) Description

Title :  CRYSTAL STRUCTURE OF ENDO-1,4-BETA-XYLANASE (NP_811807.1) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  23 Nov 09  (Deposition) - 08 Dec 09  (Release) - 08 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Endo-1, 4-Beta-Xylanase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Xylan Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Endo-1, 4-Beta-Xylanase (Np_811807. 1) From Bacteroides Thetaiotaomicron Vpi-5482 At 1. 70 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE
    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
    Gene: BT_2895
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON VPI-5482
    Organism Taxid: 226186

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:8 , GLU A:107 , HIS A:275 , HOH A:389 , HOH A:397 , HOH A:398 , HOH A:399BINDING SITE FOR RESIDUE CA A 400
2AC2SOFTWAREHOH B:2 , HOH B:7 , HOH B:20 , GLU B:107 , HIS B:275 , HOH B:437 , HOH B:568BINDING SITE FOR RESIDUE CA B 400
3AC3SOFTWAREASP B:50 , ARG B:302 , HOH B:381 , HOH B:475BINDING SITE FOR RESIDUE EDO B 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:137 -Pro A:138
2Gly A:251 -Pro A:252
3Asn A:259 -Pro A:260
4Gln A:300 -Pro A:301
5Gly B:137 -Pro B:138
6Gly B:251 -Pro B:252
7Asn B:259 -Pro B:260
8Gln B:300 -Pro B:301

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KST)

(-) Sequences/Alignments

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:291
 aligned with Q8A3Q9_BACTN | Q8A3Q9 from UniProtKB/TrEMBL  Length:330

    Alignment length:291
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329 
         Q8A3Q9_BACTN    40 SVETNYLPIADPYVMFYNNKYYAYGTGGTTAGEGFACFSSDDLKNWKREGQALSATDSYGTWGFWAPEVYYVESKKKFYLFYSAEEHICVATSTTPEGPFRQEVKQPIWSEKSIDTSLFIDDDGTPYLYFVRFTDGNVIWVAQMTDDLMSIKTETLNQCIKAEVSWELLQGKVAEGPSLLKKNGVYYLIYSANHYENKGYGVGYATSDTPMGPWVKYSKNPLLQGDAATGLVGTGHGAPFQCKDGSWKYIFHAHWSAAEIQPRTSYIKDFAISDQGVVTISGTVIKPRVLK 330
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeeeee..eeeeeee.......eeeeeee....eeeeeeeeee.hhh......eeeeeeee....eeeeeeee..eeeeeee....................eeeeeee.....eeeeeeee...eeeeeee........hhhhheeee...hhhhh.....eeeeeeeee..eeeeeeee........eeeeeee.......ee..................eeeeeee.....eeeeeee..........eeeeeeeee.....eeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kst A  40 SVETNYLPIADPYVmFYNNKYYAYGTGGTTAGEGFACFSSDDLKNWKREGQALSATDSYGTWGFWAPEVYYVESKKKFYLFYSAEEHICVATSTTPEGPFRQEVKQPIWSEKSIDTSLFIDDDGTPYLYFVRFTDGNVIWVAQmTDDLmSIKTETLNQCIKAEVSWELLQGKVAEGPSLLKKNGVYYLIYSANHYENKGYGVGYATSDTPmGPWVKYSKNPLLQGDAATGLVGTGHGAPFQCKDGSWKYIFHAHWSAAEIQPRTSYIKDFAISDQGVVTISGTVIKPRVLK 330
                                    49    |   59        69        79        89        99       109       119       129       139       149       159       169       179   |   189       199       209       219       229       239       249|      259       269       279       289       299       309       319       329 
                                         54-MSE                                                                                                                          183-MSE|                                                           250-MSE                                                                            
                                                                                                                                                                              188-MSE                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with Q8A3Q9_BACTN | Q8A3Q9 from UniProtKB/TrEMBL  Length:330

    Alignment length:291
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329 
         Q8A3Q9_BACTN    40 SVETNYLPIADPYVMFYNNKYYAYGTGGTTAGEGFACFSSDDLKNWKREGQALSATDSYGTWGFWAPEVYYVESKKKFYLFYSAEEHICVATSTTPEGPFRQEVKQPIWSEKSIDTSLFIDDDGTPYLYFVRFTDGNVIWVAQMTDDLMSIKTETLNQCIKAEVSWELLQGKVAEGPSLLKKNGVYYLIYSANHYENKGYGVGYATSDTPMGPWVKYSKNPLLQGDAATGLVGTGHGAPFQCKDGSWKYIFHAHWSAAEIQPRTSYIKDFAISDQGVVTISGTVIKPRVLK 330
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Glyco_hydro_43-3kstB01 B:46-317                                                                                                                                                                                                                                                 ------------- Pfam domains (1)
           Pfam domains (2) ------Glyco_hydro_43-3kstB02 B:46-317                                                                                                                                                                                                                                                 ------------- Pfam domains (2)
         Sec.struct. author .eee.....eeeeeeee..eeeeeee.......eeeeeee....eeeeeeeeee.hhh......eeeeeeee....eeeeeeee..eeeeeee....................eeeeeee.....eeeeeee.....eeeeeee......eeeeeeeeee...hhhhhh....eeeeeeeee..eeeeeeee........eeeeeee.......ee..................eeeeeee.....eeeeeee..........eeeeeeeee.....eeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kst B  40 SVETNYLPIADPYVmFYNNKYYAYGTGGTTAGEGFACFSSDDLKNWKREGQALSATDSYGTWGFWAPEVYYVESKKKFYLFYSAEEHICVATSTTPEGPFRQEVKQPIWSEKSIDTSLFIDDDGTPYLYFVRFTDGNVIWVAQmTDDLmSIKTETLNQCIKAEVSWELLQGKVAEGPSLLKKNGVYYLIYSANHYENKGYGVGYATSDTPmGPWVKYSKNPLLQGDAATGLVGTGHGAPFQCKDGSWKYIFHAHWSAAEIQPRTSYIKDFAISDQGVVTISGTVIKPRVLK 330
                                    49    |   59        69        79        89        99       109       119       129       139       149       159       169       179   |   189       199       209       219       229       239       249|      259       269       279       289       299       309       319       329 
                                         54-MSE                                                                                                                          183-MSE|                                                           250-MSE                                                                            
                                                                                                                                                                              188-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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: B_Fructosidase (34)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8A3Q9_BACTN | Q8A3Q9)
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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