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(-) Description

Title :  SEMET STRUCTURE OF A NOVEL CARBOHYDRATE BINDING MODULE FROM GLYCOSIDE HYDROLASE FAMILY 9 (CEL9A) FROM RUMINOCOCCUS FLAVEFACIENS FD-1
 
Authors :  I. Venditto, A. Goyal, A. Thompson, L. M. A. Ferreira, C. M. G. A. Fontes, S. Najmudin
Date :  29 Sep 14  (Deposition) - 20 Jan 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Sugar Binding Protein, Carbohydrate Binding Module, Glycoside Hydrolase Family 9, Cel9A, Cellulosome, Ruminococcus Flavefaciens Fd-1, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Venditto, A. S. Luis, M. Rydahl, J. Schuckel, V. O. Fernandes, S. Vidal-Melgosa, P. Bule, A. Goyal, V. M. R. Pires, C. G. Dourado, L. M. A. Ferreira, P. M. Coutinho, B. Henrissat, J. P. Knox, A. Basle, S. Najmudin, H. J. Gilbert, W. G. T. Willats, C. M. G. A. Fontes
Complexity Of The Ruminococcus Flavefaciens Cellulosome Reflects An Expansion In Glycan Recognition.
Proc. Natl. Acad. Sci. Usa V. 113 7136 2016
PubMed-ID: 27298375  |  Reference-DOI: 10.1073/PNAS.1601558113
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOHYDRATE BINDING MODULE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI B
    Expression System Plasmid: PET-28A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 37762
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 492-629
    Organism Scientific: RUMINOCOCCUS FLAVEFACIENS
    Organism Taxid: 641112
    Other Details: SELENOMETHIONINE DERIVATIVE
    Strain: FD-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
2BGQ1Ligand/Ion2-HYDROXY BUTANE-1,4-DIOL
3CA3Ligand/IonCALCIUM ION
4MSE2Mod. Amino AcidSELENOMETHIONINE
5P6G1Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARE2PE A:1625 , HOH A:2074BINDING SITE FOR RESIDUE CA A1627
2AC2SOFTWAREP6G A:1626BINDING SITE FOR RESIDUE CA A1628
3AC3SOFTWAREBGQ A:1630BINDING SITE FOR RESIDUE CA A1629
4AC4SOFTWARETRP A:607 , CA A:1629BINDING SITE FOR RESIDUE BGQ A1630
5AC5SOFTWAREGLU A:512 , ASP A:513 , SER A:555 , GLY A:562 , TYR A:563 , TRP A:564 , TYR A:597 , GLY A:598 , CA A:1627 , CA A:1628 , HOH A:2075 , HOH A:2143 , HOH A:2144BINDING SITE FOR RESIDUES 2PE A1625 AND P6G A1626

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4V1K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4V1K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V1K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V1K)

(-) Exons   (0, 0)

(no "Exon" information available for 4V1K)

(-) 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:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee.hhhhhhh.eeeee.hhh.......eeeeeeeee.....eeeeeeeeee..hhhhh.eee...eeeee...eeeeeee.hhhhhh........eeeeeeeee...eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v1k A 494 SDGYTIKPNKKVTYSALGEDERmIGFSYKDFGISSSEKITEVQVNISANKNIGKYVGQFGTSTTDSANGYWAmGDEITQSISGNSGTITWKVPSDISSIIQTQYGGEIKFGVWWIDCDEFTIDSVVLKLEH 624
                                   503       513  |    523       533       543       553       563  |    573       583       593       603       613       623 
                                                516-MSE                                           566-MSE
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4V1K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V1K)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

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UniProtKB/TrEMBL
        A0A140UH31_R | A0A140UH31: 4d3l 4v1l

(-) Related Entries Specified in the PDB File

4v17 STRUCTURE OF A NOVEL CARBOHYDRATE BINDING MODULE FROM GLYCOSIDE HYDROLASE FAMILY 5 GLUCANASE FROM RUMINOCOCCUS FLAVEFACIENS FD-1
4v18 SEMET STRUCTURE OF A NOVEL CARBOHYDRATE BINDING MODULE FROM GLYCOSIDE HYDROLASE FAMILY 5 GLUCANASE FROM RUMINOCOCCUS FLAVEFACIENS FD-1
4v1b STRUCTURE OF A NOVEL CARBOHYDRATE BINDING MODULE FROM GLYCOSIDE HYDROLASE FAMILY 5 GLUCANASE FROM RUMINOCOCCUS FLAVEFACIENS FD-1 COLLECTED AT THE ZN EDGE
4v1i STRUCTURE OF A NOVEL CARBOHYDRATE BINDING MODULE FROM GLYCOSIDE HYDROLASE FAMILY 5 GLUCANASE FROM RUMINOCOCCUS FLAVEFACIENS FD-1 AT MEDIUM RESOLUTION
4v1l HIGH RESOLUTION STRUCTURE OF A NOVEL CARBOHYDRATE BINDING MODULE FROM GLYCOSIDE HYDROLASE FAMILY 9 (CEL9A ) FROM RUMINOCOCCUS FLAVEFACIENS FD-1