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(-) Description

Title :  STRUCTURAL GENOMICS, PROTEIN TF1
 
Authors :  R. Zhang, I. Dementieva, J. Thorn, M. Donnelly, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  19 Oct 01  (Deposition) - 14 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, X-Ray Crystallography, Ycio, Putative Translation Factor, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, I. Dementieva, J. Thorn, M. Donnelly, A. Joachimiak
Structural Genomics, Protein Tf1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN YCIO
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YCIO
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MC1061
    Synonym: PROTEIN TF1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:57 , HIS A:63 , THR A:66 , THR A:143 , SER A:144 , ARG A:196 , HOH A:302 , HOH A:317BINDING SITE FOR RESIDUE SO4 A 207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K7J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:93 -Pro A:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K7J)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YRDCPS51163 YrdC-like domain profile.YCIO_ECOL614-200  1A:14-200
YCIO_ECOLI14-200  1A:14-200
YCIO_SHIFL14-200  1A:14-200

(-) Exons   (0, 0)

(no "Exon" information available for 1K7J)

(-) 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:206
 aligned with YCIO_ECOL6 | P0AFR5 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           YCIO_ECOL6     1 MSQFFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELSTYSFVDNVAFRLMKNNTPGNYTFILKGTKEVPRRLLQEKRKTIGMRVPSNPIAQALLEALGEPMLSTSLMLPGSEFTESDPEEIKDRLEKQVDLIIHGGYLGQKPTTVIDLTDDTPVVVREGVGDVKPFL 206
               SCOP domains d1k7ja_ A: Hypothetical protein YciO                                                                                                                                                                           SCOP domains
               CATH domains -1k7jA00 A:2-206 DHBP synthase                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------Sua5_yciO_yrdC-1k7jA01 A:22-198                                                                                                                                                  -------- Pfam domains
         Sec.struct. author ..eeee......hhhhhhhhhhhhhh...eeeee..eeeeeee..hhhhhhhhhhhhh.......eee..hhhhhhhhh..hhhhhhhhhh.....eeeeee.....hhhhh.....eeeee...hhhhhhhhhhhh..eeeee...........hhhhhhhhhh....eeee.........eeee.hhhh.eeee.....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------YRDC  PDB: A:14-200 UniProt: 14-200                                                                                                                                                        ------ PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k7j A   1 mSQFFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAmERICRIRQLPDGHNFTLmCRDLSELSTYSFVDNVAFRLmKNNTPGNYTFILKGTKEVPRRLLQEKRKTIGmRVPSNPIAQALLEALGEPmLSTSLmLPGSEFTESDPEEIKDRLEKQVDLIIHGGYLGQKPTTVIDLTDDTPVVVREGVGDVKPFL 206
                            |       10        20        30        40        50        60       |70        80        90       100       110       120|      130       140     | 150       160       170       180       190       200      
                            |                                               50-MSE            68-MSE               89-MSE                         121-MSE            140-MSE |                                                            
                            1-MSE                                                                                                                                          146-MSE                                                        


Chain A from PDB  Type:PROTEIN  Length:206
 aligned with YCIO_ECOLI | P0AFR4 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           YCIO_ECOLI     1 MSQFFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELSTYSFVDNVAFRLMKNNTPGNYTFILKGTKEVPRRLLQEKRKTIGMRVPSNPIAQALLEALGEPMLSTSLMLPGSEFTESDPEEIKDRLEKQVDLIIHGGYLGQKPTTVIDLTDDTPVVVREGVGDVKPFL 206
               SCOP domains d1k7ja_ A: Hypothetical protein YciO                                                                                                                                                                           SCOP domains
               CATH domains -1k7jA00 A:2-206 DHBP synthase                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------Sua5_yciO_yrdC-1k7jA01 A:22-198                                                                                                                                                  -------- Pfam domains
         Sec.struct. author ..eeee......hhhhhhhhhhhhhh...eeeee..eeeeeee..hhhhhhhhhhhhh.......eee..hhhhhhhhh..hhhhhhhhhh.....eeeeee.....hhhhh.....eeeee...hhhhhhhhhhhh..eeeee...........hhhhhhhhhh....eeee.........eeee.hhhh.eeee.....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------YRDC  PDB: A:14-200 UniProt: 14-200                                                                                                                                                        ------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k7j A   1 mSQFFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAmERICRIRQLPDGHNFTLmCRDLSELSTYSFVDNVAFRLmKNNTPGNYTFILKGTKEVPRRLLQEKRKTIGmRVPSNPIAQALLEALGEPmLSTSLmLPGSEFTESDPEEIKDRLEKQVDLIIHGGYLGQKPTTVIDLTDDTPVVVREGVGDVKPFL 206
                            |       10        20        30        40        50        60       |70        80        90       100       110       120|      130       140     | 150       160       170       180       190       200      
                            1-MSE                                           50-MSE            68-MSE               89-MSE                         121-MSE            140-MSE |                                                            
                                                                                                                                                                           146-MSE                                                        


Chain A from PDB  Type:PROTEIN  Length:206
 aligned with YCIO_SHIFL | P0AFR6 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           YCIO_SHIFL     1 MSQFFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELSTYSFVDNVAFRLMKNNTPGNYTFILKGTKEVPRRLLQEKRKTIGMRVPSNPIAQALLEALGEPMLSTSLMLPGSEFTESDPEEIKDRLEKQVDLIIHGGYLGQKPTTVIDLTDDTPVVVREGVGDVKPFL 206
               SCOP domains d1k7ja_ A: Hypothetical protein YciO                                                                                                                                                                           SCOP domains
               CATH domains -1k7jA00 A:2-206 DHBP synthase                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------Sua5_yciO_yrdC-1k7jA01 A:22-198                                                                                                                                                  -------- Pfam domains
         Sec.struct. author ..eeee......hhhhhhhhhhhhhh...eeeee..eeeeeee..hhhhhhhhhhhhh.......eee..hhhhhhhhh..hhhhhhhhhh.....eeeeee.....hhhhh.....eeeee...hhhhhhhhhhhh..eeeee...........hhhhhhhhhh....eeee.........eeee.hhhh.eeee.....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------YRDC  PDB: A:14-200 UniProt: 14-200                                                                                                                                                        ------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k7j A   1 mSQFFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAmERICRIRQLPDGHNFTLmCRDLSELSTYSFVDNVAFRLmKNNTPGNYTFILKGTKEVPRRLLQEKRKTIGmRVPSNPIAQALLEALGEPmLSTSLmLPGSEFTESDPEEIKDRLEKQVDLIIHGGYLGQKPTTVIDLTDDTPVVVREGVGDVKPFL 206
                            |       10        20        30        40        50        60       |70        80        90       100       110       120|      130       140     | 150       160       170       180       190       200      
                            1-MSE                                           50-MSE            68-MSE               89-MSE                         121-MSE            140-MSE |                                                            
                                                                                                                                                                           146-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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Sua5_yciO_yrdC] (2)

(-) Gene Ontology  (2, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YCIO_ECOLI | P0AFR4)
molecular function
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A   (YCIO_ECOL6 | P0AFR5)
molecular function
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.

Chain A   (YCIO_SHIFL | P0AFR6)
molecular function
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        YCIO_ECOL6 | P0AFR5: 1kk9
        YCIO_ECOLI | P0AFR4: 1kk9
        YCIO_SHIFL | P0AFR6: 1kk9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1K7J)