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(-) Description

Title :  CRYSTAL STRUCTURE OF RAFE FROM STREPTOCOCCUS PNEUMONIAE COMPLEXED WITH RAFFINOSE
 
Authors :  N. G. Paterson, A. Riboldi-Tunnicliffe, T. J. Mitchell, N. W. Isaacs
Date :  24 Aug 06  (Deposition) - 07 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C#,D#
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Complex With Raffinose, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. G. Paterson, A. Riboldi-Tunnicliffe, T. J. Mitchell, N. W. Isaacs
Crystal Structure Of Apo And Bound Forms Of Rafe From Streptococcus Pneumoniae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUGAR ABC TRANSPORTER, SUGAR-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTBL2
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SP1897
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABC#D#
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2FRU2Ligand/IonFRUCTOSE
3GLA2Ligand/IonALPHA D-GALACTOSE
4GLC2Ligand/IonALPHA-D-GLUCOSE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FRU-1Ligand/IonFRUCTOSE
3GLA-1Ligand/IonALPHA D-GALACTOSE
4GLC-1Ligand/IonALPHA-D-GLUCOSE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FRU-1Ligand/IonFRUCTOSE
3GLA-1Ligand/IonALPHA D-GALACTOSE
4GLC-1Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:65 , GLN A:67 , ASN A:165 , TRP A:246 , TRP A:348 , GLN A:350 , GLU A:356 , GLC C:2 , FRU C:3BINDING SITE FOR RESIDUE GLA C 1
2AC2SOFTWARELYS A:14 , GLU A:16 , TYR A:65 , TRP A:246 , ASP A:280 , GLA C:1 , FRU C:3BINDING SITE FOR RESIDUE GLC C 2
3AC3SOFTWAREGLN A:13 , TRP A:162 , GLU A:356 , GLA C:1 , GLC C:2BINDING SITE FOR RESIDUE FRU C 3
4AC4SOFTWARETYR B:65 , GLN B:67 , TRP B:162 , ASN B:165 , TRP B:246 , TRP B:348 , GLN B:350 , GLU B:356 , GLC D:2 , FRU D:3BINDING SITE FOR RESIDUE GLA D 1
5AC5SOFTWARELYS B:14 , GLU B:16 , TYR B:65 , TRP B:246 , ASP B:280 , GLA D:1 , FRU D:3BINDING SITE FOR RESIDUE GLC D 2
6AC6SOFTWAREGLN B:13 , TRP B:162 , GLU B:356 , GLA D:1 , GLC D:2BINDING SITE FOR RESIDUE FRU D 3
7AC7SOFTWAREGLU B:356 , ALA B:357BINDING SITE FOR RESIDUE CL B 389
8AC8SOFTWARELYS B:217BINDING SITE FOR RESIDUE CL B 390

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I58)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I58)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I58)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I58)

(-) Exons   (0, 0)

(no "Exon" information available for 2I58)

(-) 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:385
 aligned with A0A0H2URJ7_S | A0A0H2URJ7 from UniProtKB/TrEMBL  Length:419

    Alignment length:385
                                    41        51        61        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     
         A0A0H2URJ7_S    32 GTVTIEYFNQKKEMTKTLEEITRDFEKENPKIKVKVVNVPNAGEVLKTRVLAGDVPDVVNIYPQSIELQEWAKAGVFEDLSNKDYLKRVKNGYAEKYAVNEKVYNVPFTANAYGIYYNKDKFEELGLKVPETWDEFEQLVKDIVAKGQTPFGIAGADAWTLNGYNQLAFATATGGGKEANQYLRYSQPNAIKLSDPIMKDDIKVMDILRINGSKQKNWEGAGYTDVIGAFARGDVLMTPNGSWAITAINEQKPNFKIGTFMIPGKEKGQSLTVGAGDLAWSISATTKHPKEANAFVEYMTRPEVMQKYYDVDGSPTAIEGVKQAGEDSPLAGMTEYAFTDRHLVWLQQYWTSEADFHTLTMNYVLTGDKQGMVNDLNAFFNPMKA 416
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.....eee....hhhhhhhhhh.........hhhhhh....hhhhh.......ee.....eeeeeehhhhhhhh.....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhh.....eeee...........ee.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh........ee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i58 A   4 STVTIEYFNQKKEMTKTLEEITRDFEKENPKIKVKVVNVPNAGEVLKTRVLAGDVPDVVNIYPQSIELQEWAKAGVFEDLSNKDYLKRVKNGYAEKYAVNEKVYNVPFTANAYGIYYNKDKFEELGLKVPETWDEFEQLVKDIVAKGQTPFGIAGADAWTLNGYNQLAFATATGGGKEANQYLRYSQPNAIKLSDPIMKDDIKVMDILRINGSKQKNWEGAGYTDVIGAFARGDVLMTPNGSWAITAINEQKPNFKIGTFMIPGKEKGQSLTVGAGDLAWSISATTKHPKEANAFVEYMTRPEVMQKYYDVDGSPTAIEGVKQAGEDSPLAGMTEYAFTDRHLVWLQQYWTSEADFHTLTMNYVLTGDKQGMVNDLNAFFNPMKM 388
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383     


Chain B from PDB  Type:PROTEIN  Length:385
 aligned with A0A0H2URJ7_S | A0A0H2URJ7 from UniProtKB/TrEMBL  Length:419

    Alignment length:385
                                    41        51        61        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     
         A0A0H2URJ7_S    32 GTVTIEYFNQKKEMTKTLEEITRDFEKENPKIKVKVVNVPNAGEVLKTRVLAGDVPDVVNIYPQSIELQEWAKAGVFEDLSNKDYLKRVKNGYAEKYAVNEKVYNVPFTANAYGIYYNKDKFEELGLKVPETWDEFEQLVKDIVAKGQTPFGIAGADAWTLNGYNQLAFATATGGGKEANQYLRYSQPNAIKLSDPIMKDDIKVMDILRINGSKQKNWEGAGYTDVIGAFARGDVLMTPNGSWAITAINEQKPNFKIGTFMIPGKEKGQSLTVGAGDLAWSISATTKHPKEANAFVEYMTRPEVMQKYYDVDGSPTAIEGVKQAGEDSPLAGMTEYAFTDRHLVWLQQYWTSEADFHTLTMNYVLTGDKQGMVNDLNAFFNPMKA 416
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh.....eee....hhhhhhhhhh.........hhhhhhhhhhhhhh.......eee.....eeeeeehhhhhhhh.....hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.hhhhhhhhh..........hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhh.....eeee...........eee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh............................eee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i58 B   4 STVTIEYFNQKKEMTKTLEEITRDFEKENPKIKVKVVNVPNAGEVLKTRVLAGDVPDVVNIYPQSIELQEWAKAGVFEDLSNKDYLKRVKNGYAEKYAVNEKVYNVPFTANAYGIYYNKDKFEELGLKVPETWDEFEQLVKDIVAKGQTPFGIAGADAWTLNGYNQLAFATATGGGKEANQYLRYSQPNAIKLSDPIMKDDIKVMDILRINGSKQKNWEGAGYTDVIGAFARGDVLMTPNGSWAITAINEQKPNFKIGTFMIPGKEKGQSLTVGAGDLAWSISATTKHPKEANAFVEYMTRPEVMQKYYDVDGSPTAIEGVKQAGEDSPLAGMTEYAFTDRHLVWLQQYWTSEADFHTLTMNYVLTGDKQGMVNDLNAFFNPMKM 388
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383
   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 2I58)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I58)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I58)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2I58)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A0A0H2URJ7_S | A0A0H2URJ7: 2heu 2hfb 2hq0

(-) Related Entries Specified in the PDB File

2heu ATOMIC RESOLUTION APO FORM WITH POLYHISTIDINE TAG
2hfb LOW RESOLUTION APO FORM WITH POLYHISTIDINE TAG
2hq0 HIGH RESOLUTION APO FORM WITH POLYHISTIDINE TAG CLEAVED