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(-) Description

Title :  CRYSTAL STRUCTURE OF A SUSD HOMOLOG (BDI_0600) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.05 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Sep 10  (Deposition) - 03 Nov 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Susd Homolog (Yp_001301998. 1) From Parabacteroides Distasonis Atcc 8503 At 2. 05 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUSD HOMOLOG
    Atcc: 8503
    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: SEQUENCE DATABASE RESIDUES 26-553
    Gene: BDI_0600
    Organism Scientific: PARABACTEROIDES DISTASONIS ATCC 8503
    Organism Taxid: 435591
    Strain: DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:130 , ARG B:130 , ALA B:177 , HOH B:1049BINDING SITE FOR RESIDUE SO4 B 554

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P1U)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:461 -Pro A:462
2Leu A:477 -Pro A:478
3Ile B:461 -Pro B:462
4Leu B:477 -Pro B:478

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P1U)

(-) Exons   (0, 0)

(no "Exon" information available for 3P1U)

(-) 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:515
 aligned with A6L9L2_PARD8 | A6L9L2 from UniProtKB/TrEMBL  Length:553

    Alignment length:515
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548     
         A6L9L2_PARD8    39 NMNEPRLASTLRGGLIIEGNVEQRLKPLQIDFYSQMTVDGGGWGTKNYIQDDEWNNLVWEEYLKQIASINIVIRSLTEKDKDAYANTIAFARIWRVYVHTLAADKFGPMPFPAYEIVEANPPYKSLKDIYDEYFRELDAAINGFNDSAQPIFSDAGIDLIYKNDVSKWKRFANSLRLRLAVRLTEVDQEKCIAEANAAISSPAGLISDKADNAYMPPKADGSWGQDYNYTMFQITWSGPICMSKSVEKLVTNIGGVAWPQGVVNQTSGVAVSSVHPEKVDPRAPKIFQPGIENGDWKGLVYGPKAEEANTGIYQSKQCAELGFIIKDGYPYKSRPYDLFLSEEVHFLKAELYARGFIAGDAKSEYEAGVRASFATWGVTSEVDDYLTSTEKNEAGTSARYDDQQGAGNTALEKIITQKYIAGIPDLAQEGWNDKRRLNLPRLDVAVYRDQAVYNNNDKDILKSANFIKRMRYPTKESLINATEYEKGKSMLGGKGDIVSTPLWWDKNSNYCTSSK 553
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhh..hhhhhhh..ee...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.ee............eehhhhhhhhhhhhhhhhhhhh.........hhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhheee............hhhhhhh.....ee.hhhhhhhhh..............................hhhhhee...............hhhhh.hhhhhhhhh.ee...ee..ee.....eeeehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhh.....................hhhhhhhhhhhhh....hhhhhhhhhhhhh.......................hhhhh........hhhhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1u A  39 NmNEPRLASTLRGGLIIEGNVEQRLKPLQIDFYSQmTVDGGGWGTKNYIQDDEWNNLVWEEYLKQIASINIVIRSLTEKDKDAYANTIAFARIWRVYVHTLAADKFGPmPFPAYEIVEANPPYKSLKDIYDEYFRELDAAINGFNDSAQPIFSDAGIDLIYKNDVSKWKRFANSLRLRLAVRLTEVDQEKCIAEANAAISSPAGLISDKADNAYmPPKADGSWGQDYNYTmFQITWSGPICmSKSVEKLVTNIGGVAWPQGVVNQTSGVAVSSVHPEKVDPRAPKIFQPGIENGDWKGLVYGPKAEEANTGIYQSKQCAELGFIIKDGYPYKSRPYDLFLSEEVHFLKAELYARGFIAGDAKSEYEAGVRASFATWGVTSEVDDYLTSTEKNEAGTSARYDDQQGAGNTALEKIITQKYIAGIPDLAQEGWNDKRRLNLPRLDVAVYRDQAVYNNNDKDILKSANFIKRmRYPTKESLINATEYEKGKSmLGGKGDIVSTPLWWDKNSNYCTSSK 553
                             |      48        58        68     |  78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248    |  258       268|      278 |     288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548     
                             |                                74-MSE                                                                  147-MSE                                                                                                   253-MSE         269-MSE    280-MSE                                                                                                                                                                                                                             508-MSE             528-MSE                     
                            40-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:515
 aligned with A6L9L2_PARD8 | A6L9L2 from UniProtKB/TrEMBL  Length:553

    Alignment length:515
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548     
         A6L9L2_PARD8    39 NMNEPRLASTLRGGLIIEGNVEQRLKPLQIDFYSQMTVDGGGWGTKNYIQDDEWNNLVWEEYLKQIASINIVIRSLTEKDKDAYANTIAFARIWRVYVHTLAADKFGPMPFPAYEIVEANPPYKSLKDIYDEYFRELDAAINGFNDSAQPIFSDAGIDLIYKNDVSKWKRFANSLRLRLAVRLTEVDQEKCIAEANAAISSPAGLISDKADNAYMPPKADGSWGQDYNYTMFQITWSGPICMSKSVEKLVTNIGGVAWPQGVVNQTSGVAVSSVHPEKVDPRAPKIFQPGIENGDWKGLVYGPKAEEANTGIYQSKQCAELGFIIKDGYPYKSRPYDLFLSEEVHFLKAELYARGFIAGDAKSEYEAGVRASFATWGVTSEVDDYLTSTEKNEAGTSARYDDQQGAGNTALEKIITQKYIAGIPDLAQEGWNDKRRLNLPRLDVAVYRDQAVYNNNDKDILKSANFIKRMRYPTKESLINATEYEKGKSMLGGKGDIVSTPLWWDKNSNYCTSSK 553
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SusD-like-3p1uB01 B:39-545                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 -------- Pfam domains (1)
           Pfam domains (2) SusD-like-3p1uB02 B:39-545                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 -------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhh..hhhhhhh..ee...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.ee............eehhhhhhhhhhhhhhhhhhhh.........hhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhheee............hhhhhhh.....ee.hhhhhhhhh..............................hhhhhee...............hhhhh.hhhhhhhhh.ee...ee..ee.....eeeehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhh.....................hhhhhhhhhhhhh....hhhhhhhhhhhhh.......................hhhhh........hhhhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1u B  39 NmNEPRLASTLRGGLIIEGNVEQRLKPLQIDFYSQmTVDGGGWGTKNYIQDDEWNNLVWEEYLKQIASINIVIRSLTEKDKDAYANTIAFARIWRVYVHTLAADKFGPmPFPAYEIVEANPPYKSLKDIYDEYFRELDAAINGFNDSAQPIFSDAGIDLIYKNDVSKWKRFANSLRLRLAVRLTEVDQEKCIAEANAAISSPAGLISDKADNAYmPPKADGSWGQDYNYTmFQITWSGPICmSKSVEKLVTNIGGVAWPQGVVNQTSGVAVSSVHPEKVDPRAPKIFQPGIENGDWKGLVYGPKAEEANTGIYQSKQCAELGFIIKDGYPYKSRPYDLFLSEEVHFLKAELYARGFIAGDAKSEYEAGVRASFATWGVTSEVDDYLTSTEKNEAGTSARYDDQQGAGNTALEKIITQKYIAGIPDLAQEGWNDKRRLNLPRLDVAVYRDQAVYNNNDKDILKSANFIKRmRYPTKESLINATEYEKGKSmLGGKGDIVSTPLWWDKNSNYCTSSK 553
                             |      48        58        68     |  78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248    |  258       268|      278 |     288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548     
                            40-MSE                            74-MSE                                                                  147-MSE                                                                                                   253-MSE         269-MSE    280-MSE                                                                                                                                                                                                                             508-MSE             528-MSE
   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 3P1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P1U)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: TPR (230)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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