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(-) Description

Title :  CRYSTAL STRUCTURE OF XG34, AN EVOLVED XYLOGLUCAN BINDING CBM
 
Authors :  C. Divne, T. -C. Tan, H. Brumer, F. Gullfot
Date :  21 Sep 09  (Deposition) - 27 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Cbm, Xyloglucan Binding, Calcium Binding, Xylan Degradation, Hydrolase, Carbohydrate-Binding Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Gullfot, T. C. Tan, L. Von Schantz, E. N. Karlsson, M. Ohlin, H. Brumer, C. Divne
The Crystal Structure Of Xg-34, An Evolved Xyloglucan-Specific Carbohydrate-Binding Module.
Proteins V. 78 785 2009
PubMed-ID: 19950365  |  Reference-DOI: 10.1002/PROT.22642

(-) Compounds

Molecule 1 - XYLANASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: XG-34
    Mutation: YES
    Organism Common: RHODOTHERMUS OBAMENSIS
    Organism Scientific: RHODOTHERMUS MARINUS
    Organism Taxid: 29549

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA5Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:9 , GLU A:11 , GLU A:52 , LYS A:55 , ASP A:160BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREALA A:22 , TRP A:28 , ASP A:29 , HOH A:1093 , HOH A:1140 , HOH A:1228BINDING SITE FOR RESIDUE CA A 302
3AC3SOFTWAREGLY B:9 , GLU B:11 , GLU B:52 , LYS B:55 , ASP B:160BINDING SITE FOR RESIDUE CA B 301
4AC4SOFTWARELEU B:162 , HOH B:1040BINDING SITE FOR RESIDUE ACT B 401
5AC5SOFTWAREGLY C:9 , GLU C:11 , GLU C:52 , LYS C:55 , ASP C:160BINDING SITE FOR RESIDUE CA C 301
6AC6SOFTWAREHOH A:1125 , HOH B:1019 , ALA C:22 , TRP C:28 , ASP C:29 , HOH C:1029 , HOH C:1039BINDING SITE FOR RESIDUE CA C 302
7AC7SOFTWAREGLY C:9 , GLY C:161 , LEU C:162 , HOH C:1044BINDING SITE FOR RESIDUE ACT C 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:76 -Pro A:77
2Leu B:76 -Pro B:77
3Leu C:76 -Pro C:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JXS)

(-) 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:166
 aligned with Q7WTN6_RHOMR | Q7WTN6 from UniProtKB/TrEMBL  Length:997

    Alignment length:166
                                   220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370      
         Q7WTN6_RHOMR   211 ELVANINGGFESTPAGVVTDLAEGVEGWDLNVGSSVTNPPVFEVLETSDAPEGNKVLAVTVNGVGNNPWDIEATAFPVNVRPGVTYTYTIWARAEQDGAVVSFTVGNQSFQEYGRLHEQQITTEWQPFTFEFTVSDQETVIRAPIHFGYAANVGNTIYIDGLAIVD 376
               SCOP domains d3jxsa_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains 3jxsA00 A:1-166 Galactose-binding domain-like                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee..........eeeee........eeeeee........eeeeeee.....hhh.eeeeeeeee.....eeeeeeeeee....eeeeeeee.....eeeeeeeeee....eeeeeeee......eeeeeee..hhhhh.eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxs A   1 MLVANINGGFESTPAGVVTDLAEGVEGWDLNVGSSVTNPPVFEVLETSDAPEGNKVLAVTVNGVGNNPYDIHATALPVNVRPGVTYTYTIWARAEQDGAVVSFTVGNQSHDDYGRLHEQQITTEWQPFTFEFTVSDQETVIRAPIHFGFAANVGNTIYIDGLAIVD 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      


Chain B from PDB  Type:PROTEIN  Length:166
 aligned with Q7WTN6_RHOMR | Q7WTN6 from UniProtKB/TrEMBL  Length:997

    Alignment length:166
                                   220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370      
         Q7WTN6_RHOMR   211 ELVANINGGFESTPAGVVTDLAEGVEGWDLNVGSSVTNPPVFEVLETSDAPEGNKVLAVTVNGVGNNPWDIEATAFPVNVRPGVTYTYTIWARAEQDGAVVSFTVGNQSFQEYGRLHEQQITTEWQPFTFEFTVSDQETVIRAPIHFGYAANVGNTIYIDGLAIVD 376
               SCOP domains d3jxsb_ B: automated matches                                                                                                                                           SCOP domains
               CATH domains 3jxsB00 B:1-166 Galactose-binding domain-like                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee..........eeeee........eeeeee........eeeeeee.....hhh.eeeeeeeee.....eeeeeeeeee....eeeeeeee.....eeeeeeeeee....eeeeeeee......eeeeeee..hhhhh.eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxs B   1 MLVANINGGFESTPAGVVTDLAEGVEGWDLNVGSSVTNPPVFEVLETSDAPEGNKVLAVTVNGVGNNPYDIHATALPVNVRPGVTYTYTIWARAEQDGAVVSFTVGNQSHDDYGRLHEQQITTEWQPFTFEFTVSDQETVIRAPIHFGFAANVGNTIYIDGLAIVD 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      


Chain C from PDB  Type:PROTEIN  Length:166
 aligned with Q7WTN6_RHOMR | Q7WTN6 from UniProtKB/TrEMBL  Length:997

    Alignment length:166
                                   220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370      
         Q7WTN6_RHOMR   211 ELVANINGGFESTPAGVVTDLAEGVEGWDLNVGSSVTNPPVFEVLETSDAPEGNKVLAVTVNGVGNNPWDIEATAFPVNVRPGVTYTYTIWARAEQDGAVVSFTVGNQSFQEYGRLHEQQITTEWQPFTFEFTVSDQETVIRAPIHFGYAANVGNTIYIDGLAIVD 376
               SCOP domains d3jxsc_ C: automated matches                                                                                                                                           SCOP domains
               CATH domains 3jxsC00 C:1-166 Galactose-binding domain-like                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee..........eeeee........eeeeee........eeeeee......hhh.eeeeeeeee.....eeeeeeeeee....eeeeeeee.....eeeeeeeeee....eeeeeeee......eeeeeee..hhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxs C   1 MLVANINGGFESTPAGVVTDLAEGVEGWDLNVGSSVTNPPVFEVLETSDAPEGNKVLAVTVNGVGNNPYDIHATALPVNVRPGVTYTYTIWARAEQDGAVVSFTVGNQSHDDYGRLHEQQITTEWQPFTFEFTVSDQETVIRAPIHFGFAANVGNTIYIDGLAIVD 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q7WTN6_RHOMR | Q7WTN6)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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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        Q7WTN6_RHOMR | Q7WTN6: 2y64 2y6g 2y6h 2y6j 2y6k 2y6l 5dpn

(-) Related Entries Specified in the PDB File

1k45 SOLUTION STRUCTURE OF CBM4-2 WHICH IS THE PARENTAL MOLECULE OF XG34