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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 IN THE ORTHORHOMBIC FORM
 
Authors :  I. Venditto, A. Goyal, A. Thompson, L. M. A. Ferreira, C. M. G. A. Fontes, S. Najmudin
Date :  22 Oct 14  (Deposition) - 20 Jan 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
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, B, C
    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: CARBOHYDRATE BINDING MODULE, RESIDUES 492-629
    Organism Scientific: RUMINOCOCCUS FLAVEFACIENS
    Organism Taxid: 641112
    Other Details: SELENO-METHIONINE DERIVATIVE
    Strain: FD-1

 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  (9, 15)

Asymmetric Unit (9, 15)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
2CA1Ligand/IonCALCIUM ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4GOL1Ligand/IonGLYCEROL
5HHD1Ligand/Ion(3S)-3-HYDROXYHEPTANEDIOIC ACID
6MSE6Mod. Amino AcidSELENOMETHIONINE
7P6G1Ligand/IonHEXAETHYLENE GLYCOL
8PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
9PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
2CA-1Ligand/IonCALCIUM ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4GOL-1Ligand/IonGLYCEROL
5HHD-1Ligand/Ion(3S)-3-HYDROXYHEPTANEDIOIC ACID
6MSE2Mod. Amino AcidSELENOMETHIONINE
7P6G1Ligand/IonHEXAETHYLENE GLYCOL
8PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
9PG4-1Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
12PE-1Ligand/IonNONAETHYLENE GLYCOL
2CA-1Ligand/IonCALCIUM ION
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4GOL1Ligand/IonGLYCEROL
5HHD-1Ligand/Ion(3S)-3-HYDROXYHEPTANEDIOIC ACID
6MSE2Mod. Amino AcidSELENOMETHIONINE
7P6G-1Ligand/IonHEXAETHYLENE GLYCOL
8PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
9PG4-1Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 3 (4, 5)
No.NameCountTypeFull Name
12PE-1Ligand/IonNONAETHYLENE GLYCOL
2CA-1Ligand/IonCALCIUM ION
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4GOL-1Ligand/IonGLYCEROL
5HHD1Ligand/Ion(3S)-3-HYDROXYHEPTANEDIOIC ACID
6MSE2Mod. Amino AcidSELENOMETHIONINE
7P6G-1Ligand/IonHEXAETHYLENE GLYCOL
8PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
9PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:500 , LYS B:621 , HOH B:2026BINDING SITE FOR RESIDUE CA B1631
2AC2SOFTWAREGLU C:512 , ARG C:515 , TRP C:606 , PG4 C:1626 , HOH C:2058 , HOH C:2059BINDING SITE FOR RESIDUE PEG C1625
3AC3SOFTWARETYR B:563 , TRP B:606BINDING SITE FOR RESIDUE GOL B1625
4AC4SOFTWAREGLY C:562 , TRP C:564 , TYR C:597 , PEG C:1625 , HOH C:2027BINDING SITE FOR RESIDUE PG4 C1626
5AC5SOFTWARETRP C:607 , HOH C:2060BINDING SITE FOR RESIDUE HHD C1627
6AC6SOFTWAREGLU A:512 , ARG A:515 , GLY A:562 , TRP A:564 , GLN A:594 , TYR A:597 , TRP A:606 , EDO A:1628 , HOH A:2050 , HOH A:2081 , HOH A:2082 , HOH A:2096BINDING SITE FOR RESIDUES 2PE A1626 AND P6G A1627
7AC7SOFTWAREGLU A:512 , ARG A:515 , TYR A:563 , GLN A:594 , TYR A:597 , TRP A:606 , 2PE A:1626 , HOH A:2081 , HOH A:2082BINDING SITE FOR RESIDUES P6G A1627 AND EDO A1628

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D3L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4D3L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D3L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D3L)

(-) Exons   (0, 0)

(no "Exon" information available for 4D3L)

(-) 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:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eeee.hhh.....eeeee.hhh......eeeeeeeeee.....eeeee.eeee..hhhhh.eee...eeeee...eeeeeee.hhhhhh........eeeee..ee...eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4d3l A 494 SDGYTIKPNKKVTYSALGEDERmIGFSYKDFGISSSEKITEVQVNISANKNIGKYVGQFGTSTTDSANGYWAmGDEITQSISGNSGTITWKVPSDISSIIQTQYGGEIKFGVWWIDCDEFTIDSVVLKLEHH 625
                                   503       513  |    523       533       543       553       563  |    573       583       593       603       613       623  
                                                516-MSE                                           566-MSE                                                       


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee.hhh.....eeeee.hhh.......eeeeeeeee.....eeeee.eeee..hhhhh.eee...eeeee...eeeeeee.hhhhhh........eeeee..ee...eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d3l B 494 SDGYTIKPNKKVTYSALGEDERmIGFSYKDFGISSSEKITEVQVNISANKNIGKYVGQFGTSTTDSANGYWAmGDEITQSISGNSGTITWKVPSDISSIIQTQYGGEIKFGVWWIDCDEFTIDSVVLKLEH 624
                                   503       513  |    523       533       543       553       563  |    573       583       593       603       613       623 
                                                516-MSE                                           566-MSE                                                      


Chain C from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee.hhh.....eeeee.hhh.......eeeeeeeee.....eeeee.eeee..hhhhh.eee...eeeee...eeeeeee.hhhhhh........eeeee..ee...eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d3l C 494 SDGYTIKPNKKVTYSALGEDERmIGFSYKDFGISSSEKITEVQVNISANKNIGKYVGQFGTSTTDSANGYWAmGDEITQSISGNSGTITWKVPSDISSIIQTQYGGEIKFGVWWIDCDEFTIDSVVLKLEH 624
                                   503       513  |    523       533       543       553       563  |    573       583       593       603       613       623 
                                                516-MSE                                           566-MSE
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  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 4D3L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D3L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D3L)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4D3L)

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        A0A140UH31_R | A0A140UH31: 4v1k 4v1l

(-) Related Entries Specified in the PDB File

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