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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE SUGAR ISOMERASE (YP_001305149.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.68 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  01 Dec 09  (Deposition) - 22 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative Sugar Isomerase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Sugar Isomerase (Yp_001305149. 1) From Parabacteroides Distasonis Atcc 8503 At 1. 68 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE SUGAR ISOMERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 27-312
    Gene: BDI_3843
    Organism Scientific: PARABACTEROIDES DISTASONIS ATCC 8503
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 25)

Asymmetric/Biological Unit (3, 25)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:190 , ASP A:223 , HIS A:249 , GLU A:287 , HOH A:416 , HOH A:587BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWARETHR A:144 , GLY A:184 , PRO A:216 , ARG A:219 , GLN A:246 , HOH A:508 , HOH A:608 , HOH A:694BINDING SITE FOR RESIDUE PEG A 402
3AC3SOFTWARETHR A:228 , TRP A:229 , ASP B:212 , HOH B:797BINDING SITE FOR RESIDUE PEG A 403
4AC4SOFTWAREGLU B:190 , ASP B:223 , HIS B:249 , GLU B:287 , HOH B:507 , HOH B:768BINDING SITE FOR RESIDUE MG B 401
5AC5SOFTWARETHR B:228BINDING SITE FOR RESIDUE PEG B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:156 -Pro A:157
2Val B:156 -Pro B:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KWS)

(-) 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:265
 aligned with A6LIL3_PARD8 | A6LIL3 from UniProtKB/TrEMBL  Length:312

    Alignment length:265
                                    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     
         A6LIL3_PARD8    48 DLELKLSFQEGIAPGESLNEKLDFMEKLGVVGFEPGGGGLAGRVNEIKQALNGRNIKVSAICAGFKGFILSTDPAIRKECMDTMKEIIAAAGELGSTGVIIVPAFNGQVPALPHTMETRDFLCEQFNEMGTFAAQHGTSVIFEPLNRKECFYLRQVADAASLCRDINNPGVRCMGDFWHMTWEETSDMGAFISGGEYLQHVHVASRKRRSMPGEDGDADNYINGFKGLKMIGYNNYVSFECGCQGDRNVVVPAAVKLLREQWEQA 312
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......hhhhhhhhhhhh...eee.....hhhhhhhhhhhhh....ee.eee..........hhhhhhhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhh..eeeeee...........hhhhh.hhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kws A  48 DLELKLSFQEGIAPGESLNEKLDFmEKLGVVGFEPGGGGLAGRVNEIKQALNGRNIKVSAICAGFKGFILSTDPAIRKECmDTmKEIIAAAGELGSTGVIIVPAFNGQVPALPHTmETRDFLCEQFNEmGTFAAQHGTSVIFEPLNRKECFYLRQVADAASLCRDINNPGVRCmGDFWHmTWEETSDmGAFISGGEYLQHVHVASRKRRSmPGEDGDADNYINGFKGLKmIGYNNYVSFECGCQGDRNVVVPAAVKLLREQWEQA 312
                                    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     
                                                   72-MSE                                                 128-MSE                            163-MSE      176-MSE                                      221-MSE |     235-MSE                258-MSE            277-MSE                               
                                                                                                             131-MSE                                                                                         227-MSE                                                                                 


Chain B from PDB  Type:PROTEIN  Length:265
 aligned with A6LIL3_PARD8 | A6LIL3 from UniProtKB/TrEMBL  Length:312

    Alignment length:265
                                    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     
         A6LIL3_PARD8    48 DLELKLSFQEGIAPGESLNEKLDFMEKLGVVGFEPGGGGLAGRVNEIKQALNGRNIKVSAICAGFKGFILSTDPAIRKECMDTMKEIIAAAGELGSTGVIIVPAFNGQVPALPHTMETRDFLCEQFNEMGTFAAQHGTSVIFEPLNRKECFYLRQVADAASLCRDINNPGVRCMGDFWHMTWEETSDMGAFISGGEYLQHVHVASRKRRSMPGEDGDADNYINGFKGLKMIGYNNYVSFECGCQGDRNVVVPAAVKLLREQWEQA 312
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------AP_endonuc_2-3kwsB01 B:69-264                                                                                                                                                                       ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---------------------AP_endonuc_2-3kwsB02 B:69-264                                                                                                                                                                       ------------------------------------------------ Pfam domains (2)
         Sec.struct. author ....eeeee.......hhhhhhhhhhhh...eee....hhhhhhhhhhhhhh....ee.eee..........hhhhhhhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhh..eeeeee...........hhhhh.hhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kws B  48 DLELKLSFQEGIAPGESLNEKLDFmEKLGVVGFEPGGGGLAGRVNEIKQALNGRNIKVSAICAGFKGFILSTDPAIRKECmDTmKEIIAAAGELGSTGVIIVPAFNGQVPALPHTmETRDFLCEQFNEmGTFAAQHGTSVIFEPLNRKECFYLRQVADAASLCRDINNPGVRCmGDFWHmTWEETSDmGAFISGGEYLQHVHVASRKRRSmPGEDGDADNYINGFKGLKmIGYNNYVSFECGCQGDRNVVVPAAVKLLREQWEQA 312
                                    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     
                                                   72-MSE                                                 128-MSE                            163-MSE      176-MSE                                      221-MSE |     235-MSE                258-MSE            277-MSE                               
                                                                                                             131-MSE                                                                                         227-MSE
   Legend:   → Mismatch (orange background)
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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 3KWS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A6LIL3_PARD8 | A6LIL3)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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