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(-) Description

Title :  THE X-RAY CRYSTAL STRUCTURE OF TANDEM CBM51 MODULES OF SP3GH98, THE FAMILY 98 GLYCOSIDE HYDROLASE FROM STREPTOCOCCUS PNEUMONIAE SP3-BS71
 
Authors :  M. A. Higgins, E. Ficko-Blean, C. Wright, P. J. Meloncelli, T. L. Lowary A. B. Boraston
Date :  18 Apr 11  (Deposition) - 22 Jun 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Carbohydrate-Binding Module, Blood Group Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Higgins, E. Ficko-Blean, C. Wright, P. J. Meloncelli, T. L. Lowary, A. B. Boraston
The Overall Architecture And Receptor Binding Of Pneumococcal Carbohydrate Antigen Hydrolyzing Enzymes.
J. Mol. Biol. V. 411 1017 2011
PubMed-ID: 21767550  |  Reference-DOI: 10.1016/J.JMB.2011.06.035

(-) Compounds

Molecule 1 - BLOOD GROUP A-AND B-CLEAVING ENDO-BETA-GALACTOSIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Fragment: CBM51-1.2, RESIDUES 66-413
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406556
    Other Details: TANDEM FAMILY 51 CBMS
    Strain: SP3-BS71

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:161 , ALA A:211 , HIS A:214 , ASP A:218 , HOH A:2121 , HOH A:2124BINDING SITE FOR RESIDUE CA A1413
2AC2SOFTWAREVAL B:161 , ALA B:211 , HIS B:214 , ASP B:218 , HOH B:2100 , HOH B:2105BINDING SITE FOR RESIDUE CA B1412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YGL)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:126 -Pro A:127
2Asn A:308 -Pro A:309
3Ser B:126 -Pro B:127
4Asn B:308 -Pro B:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YGL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YGL)

(-) Exons   (0, 0)

(no "Exon" information available for 2YGL)

(-) 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:351
 aligned with C1CB04_STRP7 | C1CB04 from UniProtKB/TrEMBL  Length:1005

    Alignment length:351
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411 
         C1CB04_STRP7    62 DKEMTYLSDMDWSSATHGDIDKTKTVQKDAPFTTGNKGEHTKISLLTSDDKVKYFDKGIGTVADSPSVISYDISGQGFEKFETYIGIDQSANSSRSDHAVVDRIEIEIDGKVVYSSSVTNPEGFRYNTQAQFISVTIPQNAKKISLKSFAGEHTWGDEVVFADAKLIKTVSTQTITPDLLNKGINGGVYLSDLEWVDATHGDDDKSKTVQKDKPFTPGNNGSNNKIKLLIDGKEVEFNKGLGTVASNPSSIKYDVSGANVTRFISYVGIDRSANHLNSDYADIQKFEVVADGKVIYSSDSKYPKGIKYDTSAFLVDVEIPKDTQTIELKSYSGKHTWADELVLGGALFMAN 412
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhh...ee...........ee..hhhhhhhh....eeee.hhh.eeee..eeeee....eeeeee.......eeeeeeee...............eeeeee..eeeee...............eeeeee......eeeeeee........eeeeeeeeeeee......hhhhhhhh...eee.hhh...ee...........ee..hhhhhhh.....eeeee..eeeee..eee......eeeeee.....eeeeeeeeee.............eeeeeeee..eeeee...............eeeeee......eeeeeeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ygl A  62 HMASTYLSDMDWSSATHGDIDKTKTVQKDAPFTTGNKGEHTKISLLTSDDKVKYFDKGIGTVADSPSVISYDISGQGFEKFETYIGIDQSANSSRSDHAVVDRIEIEIDGKVVYSSSVTNPEGFRYNTQAQFISVTIPQNAKKISLKSFAGEHTWGDEVVFADAKLIKTVSTQTITPDLLNKGINGGVYLSDLEWVDATHGDDDKSKTVQKDKPFTPGNNGSNNKIKLLIDGKEVEFNKGLGTVASNPSSIKYDVSGANVTRFISYVGIDRSANHLNSDYADIQKFEVVADGKVIYSSDSKYPKGIKYDTSAFLVDVEIPKDTQTIELKSYSGKHTWADELVLGGALFMAN 412
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411 


Chain B from PDB  Type:PROTEIN  Length:350
 aligned with C1CB04_STRP7 | C1CB04 from UniProtKB/TrEMBL  Length:1005

    Alignment length:350
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411
         C1CB04_STRP7    62 DKEMTYLSDMDWSSATHGDIDKTKTVQKDAPFTTGNKGEHTKISLLTSDDKVKYFDKGIGTVADSPSVISYDISGQGFEKFETYIGIDQSANSSRSDHAVVDRIEIEIDGKVVYSSSVTNPEGFRYNTQAQFISVTIPQNAKKISLKSFAGEHTWGDEVVFADAKLIKTVSTQTITPDLLNKGINGGVYLSDLEWVDATHGDDDKSKTVQKDKPFTPGNNGSNNKIKLLIDGKEVEFNKGLGTVASNPSSIKYDVSGANVTRFISYVGIDRSANHLNSDYADIQKFEVVADGKVIYSSDSKYPKGIKYDTSAFLVDVEIPKDTQTIELKSYSGKHTWADELVLGGALFMA 411
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NPCBM-2yglB01 B:244-411                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NPCBM-2yglB02 B:244-411                                                                                                                                                  Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NPCBM-2yglB03 B:244-411                                                                                                                                                  Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NPCBM-2yglB04 B:244-411                                                                                                                                                  Pfam domains (4)
         Sec.struct. author .eeeee.hhh...ee...........ee..hhhhhhh.....eeee.hhh.eeee..eee......eeeeee.......eeeeeeee...............eeeeee..eeeee...............eeeeee......eeeeeee.........eeeeeeeeeee......hhhhhhhh...eee.hhh...ee...........ee..hhhhhhh.....eeeee..eeeee..eeeee....eeeeee.......eeeeeee..............eeeeeeee..eeeee...............eeeeee......eeeeeeee.......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ygl B  62 HMASTYLSDMDWSSATHGDIDKTKTVQKDAPFTTGNKGEHTKISLLTSDDKVKYFDKGIGTVADSPSVISYDISGQGFEKFETYIGIDQSANSSRSDHAVVDRIEIEIDGKVVYSSSVTNPEGFRYNTQAQFISVTIPQNAKKISLKSFAGEHTWGDEVVFADAKLIKTVSTQTITPDLLNKGINGGVYLSDLEWVDATHGDDDKSKTVQKDKPFTPGNNGSNNKIKLLIDGKEVEFNKGLGTVASNPSSIKYDVSGANVTRFISYVGIDRSANHLNSDYADIQKFEVVADGKVIYSSDSKYPKGIKYDTSAFLVDVEIPKDTQTIELKSYSGKHTWADELVLGGALFMA 411
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411
   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 2YGL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YGL)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: NPCBM] (4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2YGL)

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(-) Related Entries Specified in the PDB File

2ygm THE X-RAY CRYSTAL STRUCTURE OF TANDEM CBM51 MODULES OF SP3GH98, THE FAMILY 98 GLYCOSIDE HYDROLASE FROM STREPTOCOCCUS PNEUMONIAE SP3-BS71, IN COMPLEX WITH THE BLOOD GROUP B ANTIGEN