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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE ADHESIN (YP_001304413.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.41 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  26 Jan 10  (Deposition) - 02 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Lipoprotein, Adhesin, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Adhesin (Yp_001304413. 1) From Parabacteroides Distasonis Atcc 8503 At 2. 41 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ADHESIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BDI_3085
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:53 , TYR B:54 , GLU B:55 , THR B:62 , LYS B:102 , THR B:103 , ASN B:104 , ASN B:122BINDING SITE FOR RESIDUE PEG B 2
2AC2SOFTWARETRP A:107 , GLY A:127 , ASP A:128 , HOH A:270 , HOH A:311 , TRP B:107 , GLY B:127 , ASP B:128 , GLU B:129BINDING SITE FOR RESIDUE PEG B 4
3AC3SOFTWAREASN C:135 , ALA C:136BINDING SITE FOR RESIDUE CL C 1
4AC4SOFTWARETHR C:126 , GLY C:127 , VAL C:148 , GLU C:167BINDING SITE FOR RESIDUE PEG C 3
5AC5SOFTWARELYS C:230 , ASN C:232 , GLN C:248BINDING SITE FOR RESIDUE PEG C 5
6AC6SOFTWAREGLN A:141 , LYS A:143 , ASN C:53 , GLU C:55 , ILE C:100 , LYS C:102 , THR C:103 , ASN C:122BINDING SITE FOR RESIDUE PGE C 6

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:243 -Pro A:244
2Gly B:243 -Pro B:244
3Gly C:243 -Pro C:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LJY)

(-) 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:239
 aligned with A6LGH7_PARD8 | A6LGH7 from UniProtKB/TrEMBL  Length:262

    Alignment length:239
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252         
         A6LGH7_PARD8    23 DHVKGDGKLTSKKISVADYNEIKVDGVIDFNYEQSDDPSTVEVTVDQNLHPYVNIEVKDRVLTIAFKGAKVDHFTKFIVKTNSKWLAAAKVSGNANFMVNSPLTGDETVIKANANSLVQLKETVTVGKLDLNVSGSANMVVNHLEADKIECDIDGSGSITIKKGNAKEGDYSIVSSGDIHAFGLAVPQLSCKVTGNGLAEVHATDNLKANVVGKGNIRYKGPTAVQQRIIGKGTVEEVK 261
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeeeee.....eeee....eeeeee.....eeeeeee.hhhh.eeeeee..eeeeee...eeee...eeeeeee....eeee....eeee...eeeeeeeeee....eeee...eeeeeeeeee....eeee..eeeeeeeeee....eeee..eeeeeeeeee....eeeeeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeee...eeeeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ljy A  23 DHVKGDGKLTSKKISVADYNEIKVDGVIDFNYEQSDDPSTVEVTVDQNLHPYVNIEVKDRVLTIAFKGAKVDHFTKFIVKTNSKWLAAAKVSGNANFmVNSPLTGDETVIKANANSLVQLKETVTVGKLDLNVSGSANmVVNHLEADKIECDIDGSGSITIKKGNAKEGDYSIVSSGDIHAFGLAVPQLSCKVTGNGLAEVHATDNLKANVVGKGNIRYKGPTAVQQRIIGKGTVEEVK 261
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252         
                                                                                                                           120-MSE                                  161-MSE                                                                                                


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with A6LGH7_PARD8 | A6LGH7 from UniProtKB/TrEMBL  Length:262

    Alignment length:238
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        
         A6LGH7_PARD8    23 DHVKGDGKLTSKKISVADYNEIKVDGVIDFNYEQSDDPSTVEVTVDQNLHPYVNIEVKDRVLTIAFKGAKVDHFTKFIVKTNSKWLAAAKVSGNANFMVNSPLTGDETVIKANANSLVQLKETVTVGKLDLNVSGSANMVVNHLEADKIECDIDGSGSITIKKGNAKEGDYSIVSSGDIHAFGLAVPQLSCKVTGNGLAEVHATDNLKANVVGKGNIRYKGPTAVQQRIIGKGTVEEV 260
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeeeee.....eeee....eeeeee.....eeeeeee.hhhh.eeeeee..eeeeee...eeee...eeeeeee....eeee....eeee...eeeeeeeeee....eeee...eeeeeeeeee....eeee..eeeeeeeeee....eeee..eeeeeeeeee....eeeeeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeee...eeeeeee...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ljy B  23 DHVKGDGKLTSKKISVADYNEIKVDGVIDFNYEQSDDPSTVEVTVDQNLHPYVNIEVKDRVLTIAFKGAKVDHFTKFIVKTNSKWLAAAKVSGNANFmVNSPLTGDETVIKANANSLVQLKETVTVGKLDLNVSGSANmVVNHLEADKIECDIDGSGSITIKKGNAKEGDYSIVSSGDIHAFGLAVPQLSCKVTGNGLAEVHATDNLKANVVGKGNIRYKGPTAVQQRIIGKGTVEEV 260
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        
                                                                                                                           120-MSE                                  161-MSE                                                                                               


Chain C from PDB  Type:PROTEIN  Length:239
 aligned with A6LGH7_PARD8 | A6LGH7 from UniProtKB/TrEMBL  Length:262

    Alignment length:239
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252         
         A6LGH7_PARD8    23 DHVKGDGKLTSKKISVADYNEIKVDGVIDFNYEQSDDPSTVEVTVDQNLHPYVNIEVKDRVLTIAFKGAKVDHFTKFIVKTNSKWLAAAKVSGNANFMVNSPLTGDETVIKANANSLVQLKETVTVGKLDLNVSGSANMVVNHLEADKIECDIDGSGSITIKKGNAKEGDYSIVSSGDIHAFGLAVPQLSCKVTGNGLAEVHATDNLKANVVGKGNIRYKGPTAVQQRIIGKGTVEEVK 261
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------DUF2807-3ljyC01 C:40-244                                                                                                                                                                                     ----------------- Pfam domains (1)
           Pfam domains (2) -----------------DUF2807-3ljyC02 C:40-244                                                                                                                                                                                     ----------------- Pfam domains (2)
           Pfam domains (3) -----------------DUF2807-3ljyC03 C:40-244                                                                                                                                                                                     ----------------- Pfam domains (3)
         Sec.struct. author .eee....eeeeeee.....eeee....eeeeee.....eeeeeee.hhhh.eeeeee..eeeeee...eeee....eeeeee....eeee....eeee...eeeeeeeeee....eeee...eeeeeeeeee....eeee..eeeeeeeeee....eeee..eeeeeeeeee....eeeeeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeee...eeeeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ljy C  23 DHVKGDGKLTSKKISVADYNEIKVDGVIDFNYEQSDDPSTVEVTVDQNLHPYVNIEVKDRVLTIAFKGAKVDHFTKFIVKTNSKWLAAAKVSGNANFmVNSPLTGDETVIKANANSLVQLKETVTVGKLDLNVSGSANmVVNHLEADKIECDIDGSGSITIKKGNAKEGDYSIVSSGDIHAFGLAVPQLSCKVTGNGLAEVHATDNLKANVVGKGNIRYKGPTAVQQRIIGKGTVEEVK 261
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252         
                                                                                                                           120-MSE                                  161-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 3LJY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: 6_Hairpin (120)

(-) Gene Ontology  (0, 0)

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

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