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(-) Description

Title :  CRYSTAL STRUCTURE OF ABC SUGAR TRANSPORTER SUBUNIT FROM RHODOBACTER SPHAEROIDES 2.4.1
 
Authors :  Y. Patskovsky, S. Ozyurt, M. Dickey, J. Do, S. R. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Structural Genomix Research Consortium (Nysgxrc), New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  18 Dec 09  (Deposition) - 05 Jan 10  (Release) - 05 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B  (1x)
Biol. Unit 6:  C,D  (1x)
Keywords :  Sugar Binding/Transporter, Structural Genomics, Psi, Protein Structure Initiative, Nysgrc, Unknown Ligand, New York Structural Genomix Research Consortium, Nysgxrc, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, S. Ozyurt, M. Dickey, J. Do, S. R. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Abc Sugar Transporter From Rhodobacter Sphaeroides
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ABC SUGAR (RIBOSE) TRANSPORTER, PERIPLASMIC SUBSTRATE-BINDING SUBUNIT
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RHOS4_09560, RSP_2365
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 272943
    Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
    Synonym: PERIPLASMIC SUGAR BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): AB  
Biological Unit 6 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1UNL4Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1UNL2Ligand/IonUNKNOWN LIGAND
Biological Unit 6 (1, 2)
No.NameCountTypeFull Name
1UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (0, 0)

(no "Site" information available for 3L49)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:166 -A:224
2B:166 -B:224
3C:166 -C:224
4D:166 -D:224

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Glu A:187 -Pro A:188
2Ile A:194 -Pro A:195
3Glu B:187 -Pro B:188
4Ile B:194 -Pro B:195
5Glu C:187 -Pro C:188
6Ile C:194 -Pro C:195
7Glu D:187 -Pro D:188
8Ile D:194 -Pro D:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L49)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L49)

(-) Exons   (0, 0)

(no "Exon" information available for 3L49)

(-) 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:282
 aligned with Q3J3W0_RHOS4 | Q3J3W0 from UniProtKB/TrEMBL  Length:320

    Alignment length:282
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307  
         Q3J3W0_RHOS4    28 TLEGKTIGITAIGTDHDWDLKAYQAQIAEIERLGGTAIALDAGRNDQTQVSQIQTLIAQKPDAIIEQLGNLDVLNPWLQKINDAGIPLFTVDTATPHAINNTTSNNYSIGAELALQMVADLGGKGNVLVFNGFYSVPVCKIRYDQMKYVLEAFPDVKIIEPELRDVIPNTIQSAYSNVTDMLTKYPNEGDVGAIWACWDVPMIGATQALQAAGRTDIRTYGVDGSPEFVEMVADPESPAGAVAAQQPSEIGKLAVQNVARHLAGQEVKPFTFAPAVLITKEN 309
               SCOP domains d3l49a_ A: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeee........eeeeehhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh......eeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l49 A  28 SLEGKTIGITAIGTDHDWDLKAYQAQIAEIERLGGTAIALDAGRNDQTQVSQIQTLIAQKPDAIIEQLGNLDVLNPWLQKINDAGIPLFTVDTATPHAINNTTSNNYSIGAELALQMVADLGGKGNVLVFNGFYSVPVCKIRYDQMKYVLEAFPDVKIIEPELRDVIPNTIQSAYSNVTDMLTKYPNEGDVGAIWACWDVPMIGATQALQAAGRTDIRTYGVDGSPEFVEMVADPESPAGAVAAQQPSEIGKLAVQNVARHLAGQEVKPFTFAPAVLITKEN 309
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307  


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with Q3J3W0_RHOS4 | Q3J3W0 from UniProtKB/TrEMBL  Length:320

    Alignment length:282
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307  
         Q3J3W0_RHOS4    28 TLEGKTIGITAIGTDHDWDLKAYQAQIAEIERLGGTAIALDAGRNDQTQVSQIQTLIAQKPDAIIEQLGNLDVLNPWLQKINDAGIPLFTVDTATPHAINNTTSNNYSIGAELALQMVADLGGKGNVLVFNGFYSVPVCKIRYDQMKYVLEAFPDVKIIEPELRDVIPNTIQSAYSNVTDMLTKYPNEGDVGAIWACWDVPMIGATQALQAAGRTDIRTYGVDGSPEFVEMVADPESPAGAVAAQQPSEIGKLAVQNVARHLAGQEVKPFTFAPAVLITKEN 309
               SCOP domains d3l49b_ B: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeee........eeeeehhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh......eeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l49 B  28 SLEGKTIGITAIGTDHDWDLKAYQAQIAEIERLGGTAIALDAGRNDQTQVSQIQTLIAQKPDAIIEQLGNLDVLNPWLQKINDAGIPLFTVDTATPHAINNTTSNNYSIGAELALQMVADLGGKGNVLVFNGFYSVPVCKIRYDQMKYVLEAFPDVKIIEPELRDVIPNTIQSAYSNVTDMLTKYPNEGDVGAIWACWDVPMIGATQALQAAGRTDIRTYGVDGSPEFVEMVADPESPAGAVAAQQPSEIGKLAVQNVARHLAGQEVKPFTFAPAVLITKEN 309
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307  


Chain C from PDB  Type:PROTEIN  Length:282
 aligned with Q3J3W0_RHOS4 | Q3J3W0 from UniProtKB/TrEMBL  Length:320

    Alignment length:282
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307  
         Q3J3W0_RHOS4    28 TLEGKTIGITAIGTDHDWDLKAYQAQIAEIERLGGTAIALDAGRNDQTQVSQIQTLIAQKPDAIIEQLGNLDVLNPWLQKINDAGIPLFTVDTATPHAINNTTSNNYSIGAELALQMVADLGGKGNVLVFNGFYSVPVCKIRYDQMKYVLEAFPDVKIIEPELRDVIPNTIQSAYSNVTDMLTKYPNEGDVGAIWACWDVPMIGATQALQAAGRTDIRTYGVDGSPEFVEMVADPESPAGAVAAQQPSEIGKLAVQNVARHLAGQEVKPFTFAPAVLITKEN 309
               SCOP domains d3l49c_ C: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh...eeee........eeee.hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhh....eee..........hhhhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh......eee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l49 C  28 SLEGKTIGITAIGTDHDWDLKAYQAQIAEIERLGGTAIALDAGRNDQTQVSQIQTLIAQKPDAIIEQLGNLDVLNPWLQKINDAGIPLFTVDTATPHAINNTTSNNYSIGAELALQMVADLGGKGNVLVFNGFYSVPVCKIRYDQMKYVLEAFPDVKIIEPELRDVIPNTIQSAYSNVTDMLTKYPNEGDVGAIWACWDVPMIGATQALQAAGRTDIRTYGVDGSPEFVEMVADPESPAGAVAAQQPSEIGKLAVQNVARHLAGQEVKPFTFAPAVLITKEN 309
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307  


Chain D from PDB  Type:PROTEIN  Length:282
 aligned with Q3J3W0_RHOS4 | Q3J3W0 from UniProtKB/TrEMBL  Length:320

    Alignment length:282
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307  
         Q3J3W0_RHOS4    28 TLEGKTIGITAIGTDHDWDLKAYQAQIAEIERLGGTAIALDAGRNDQTQVSQIQTLIAQKPDAIIEQLGNLDVLNPWLQKINDAGIPLFTVDTATPHAINNTTSNNYSIGAELALQMVADLGGKGNVLVFNGFYSVPVCKIRYDQMKYVLEAFPDVKIIEPELRDVIPNTIQSAYSNVTDMLTKYPNEGDVGAIWACWDVPMIGATQALQAAGRTDIRTYGVDGSPEFVEMVADPESPAGAVAAQQPSEIGKLAVQNVARHLAGQEVKPFTFAPAVLITKEN 309
               SCOP domains d3l49d_ D: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeee........eeee.hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhhh.......eee...hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh......eee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l49 D  28 SLEGKTIGITAIGTDHDWDLKAYQAQIAEIERLGGTAIALDAGRNDQTQVSQIQTLIAQKPDAIIEQLGNLDVLNPWLQKINDAGIPLFTVDTATPHAINNTTSNNYSIGAELALQMVADLGGKGNVLVFNGFYSVPVCKIRYDQMKYVLEAFPDVKIIEPELRDVIPNTIQSAYSNVTDMLTKYPNEGDVGAIWACWDVPMIGATQALQAAGRTDIRTYGVDGSPEFVEMVADPESPAGAVAAQQPSEIGKLAVQNVARHLAGQEVKPFTFAPAVLITKEN 309
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L49)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3L49)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3L49)

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  Cis Peptide Bonds
    Glu A:187 - Pro A:188   [ RasMol ]  
    Glu B:187 - Pro B:188   [ RasMol ]  
    Glu C:187 - Pro C:188   [ RasMol ]  
    Glu D:187 - Pro D:188   [ RasMol ]  
    Ile A:194 - Pro A:195   [ RasMol ]  
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  3l49
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