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(-) Description

Title :  CRYSTAL STRUCTURE OF ABC-TYPE SUGAR TRANSPORT SYSTEM, PERIPLASMIC COMPONENT FROM EXIGUOBACTERIUM SIBIRICUM
 
Authors :  A. A. Fedorov, E. V. Fedorov, R. Toro, J. M. Sauder, S. K. Burley, S. C. Alm York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  25 Dec 09  (Deposition) - 12 Jan 10  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Nysgrc, Target 11006S, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Abc-Type Sugar Transport System, Periplasmic Component From Exiguobacterium Sibiricum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ABC-TYPE SUGAR TRANSPORT SYSTEM PERIPLASMIC COMPONENT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: EXIG_0838
    Organism Scientific: EXIGUOBACTERIUM SIBIRICUM
    Organism Taxid: 262543
    Strain: DSM 17290 / JCM 13490 / 255-15
    Synonym: PERIPLASMIC BINDING PROTEIN/LACI TRANSCRIPTIONAL REGULATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:25 , GLN A:248 , SER A:249 , ALA A:250 , GLU A:251 , HOH A:318BINDING SITE FOR RESIDUE SO4 A 294
2AC2SOFTWAREARG B:25 , GLN B:248 , SER B:249 , ALA B:250 , GLU B:251 , HOH B:317 , HOH B:333BINDING SITE FOR RESIDUE SO4 B 294

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L6U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L6U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L6U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L6U)

(-) Exons   (0, 0)

(no "Exon" information available for 3L6U)

(-) 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:274
 aligned with B1YL86_EXIS2 | B1YL86 from UniProtKB/TrEMBL  Length:317

    Alignment length:274
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    
         B1YL86_EXIS2    35 NIVGFTIVNDKHEFAQRLINAFKAEAKANKYEALVATSQNSRISEREQILEFVHLKVDAIFITTLDDVYIGSAIEEAKKAGIPVFAIDRMIRSDAVVSSITSNNQMIGEQLASYIKNELIKQTGRSTGRIVEITGTANVYTTNERHRGFLKGIENEPTLSIVDSVSGNYDPVTSERVMRQVIDSGIPFDAVYCHNDDIAMGVLEALKKAKISGKIVVGIDGNRAILEAVDMKSMDATVVQSAEEMMKVAFSALKLHTKNKKIPDRFYTYSYLYD 308
               SCOP domains d3l6ua_ A: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhh...eeee..........eeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6u A   9 NIVGFTIVNDKHEFAQRLINAFKAEAKANKYEALVATSQNSRISEREQILEFVHLKVDAIFITTLDDVYIGSAIEEAKKAGIPVFAIDRmIRSDAVVSSITSNNQmIGEQLASYIKNELIKQTGRSTGRIVEITGTANVYTTNERHRGFLKGIENEPTLSIVDSVSGNYDPVTSERVmRQVIDSGIPFDAVYCHNDDIAmGVLEALKKAKISGKIVVGIDGNRAILEAVDmKSmDATVVQSAEEmmKVAFSALKLHTKNKKIPDRFYTYSYLYD 282
                                    18        28        38        48        58        68        78        88        98       108     | 118       128       138       148       158       168       178       188       198       208       218       228       238|  |   248    || 258       268       278    
                                                                                                                    98-MSE         114-MSE                                                                 186-MSE               208-MSE                        239-MSE       253-MSE                         
                                                                                                                                                                                                                                                                   242-MSE     254-MSE                        


Chain B from PDB  Type:PROTEIN  Length:274
 aligned with B1YL86_EXIS2 | B1YL86 from UniProtKB/TrEMBL  Length:317

    Alignment length:274
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    
         B1YL86_EXIS2    35 NIVGFTIVNDKHEFAQRLINAFKAEAKANKYEALVATSQNSRISEREQILEFVHLKVDAIFITTLDDVYIGSAIEEAKKAGIPVFAIDRMIRSDAVVSSITSNNQMIGEQLASYIKNELIKQTGRSTGRIVEITGTANVYTTNERHRGFLKGIENEPTLSIVDSVSGNYDPVTSERVMRQVIDSGIPFDAVYCHNDDIAMGVLEALKKAKISGKIVVGIDGNRAILEAVDMKSMDATVVQSAEEMMKVAFSALKLHTKNKKIPDRFYTYSYLYD 308
               SCOP domains d3l6ub_ B: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Peripla_BP_4-3l6uB01 B:11-269                                                                                                                                                                                                                                      ------------- Pfam domains (1)
           Pfam domains (2) --Peripla_BP_4-3l6uB02 B:11-269                                                                                                                                                                                                                                      ------------- Pfam domains (2)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhh...eeee........eeeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6u B   9 NIVGFTIVNDKHEFAQRLINAFKAEAKANKYEALVATSQNSRISEREQILEFVHLKVDAIFITTLDDVYIGSAIEEAKKAGIPVFAIDRmIRSDAVVSSITSNNQmIGEQLASYIKNELIKQTGRSTGRIVEITGTANVYTTNERHRGFLKGIENEPTLSIVDSVSGNYDPVTSERVmRQVIDSGIPFDAVYCHNDDIAmGVLEALKKAKISGKIVVGIDGNRAILEAVDmKSmDATVVQSAEEmmKVAFSALKLHTKNKKIPDRFYTYSYLYD 282
                                    18        28        38        48        58        68        78        88        98       108     | 118       128       138       148       158       168       178       188       198       208       218       228       238|  |   248    || 258       268       278    
                                                                                                                    98-MSE         114-MSE                                                                 186-MSE               208-MSE                        239-MSE       253-MSE                         
                                                                                                                                                                                                                                                                   242-MSE     254-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L6U)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Periplas_BP (97)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B1YL86_EXIS2 | B1YL86)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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