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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  HFQ PROTEIN FROM PSEUDOMONAS AERUGINOSA. HIGH-SALT CRYSTALS
 
Authors :  A. D. Nikulin, E. A. Stolboushkina, A. A. Perederina, I. M. Vassilieva, U. Blaesi, I. Moll, G. Kachalova, S. Yokoyama, D. Vassylyev, M. Garber S. V. Nikonov, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  16 Jul 04  (Deposition) - 25 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hfq, Hf1, Sm-Like Bacterial Protein, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Nikulin, E. Stolboushkina, A. Perederina, I. Vassilieva, U. Blaesi, I. Moll, G. Kachalova, S. Yokoyama, D. Vassylyev, M. Garber, S. Nikonov
Structure Of Pseudomonas Aeruginosa Hfq Protein.
Acta Crystallogr. , Sect. D V. 61 141 2005
PubMed-ID: 15681864  |  Reference-DOI: 10.1107/S0907444904030008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HFQ PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: DH5
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HFQ
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1U1T)

(-) Sites  (0, 0)

(no "Site" information available for 1U1T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U1T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U1T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U1T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U1T)

(-) Exons   (0, 0)

(no "Exon" information available for 1U1T)

(-) 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:66
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:66
                                    15        25        35        45        55        65      
             HFQ_PSEAE    6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
               SCOP domains d1u1ta_ A: Pleiotropic translational regulator Hfq                 SCOP domains
               CATH domains 1u1tA00 A:6-71  [code=2.30.30.100, no name defined]                CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  1u1t A  6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
                                    15        25        35        45        55        65      


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:66
                                    14        24        34        44        54        64      
             HFQ_PSEAE    5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
               SCOP domains d1u1tb_ B: Pleiotropic translational regulator Hfq                 SCOP domains
               CATH domains 1u1tB00 B:5-70  [code=2.30.30.100, no name defined]                CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee....eeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  1u1t B  5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
                                    14        24        34        44        54        64      


Chain C from PDB  Type:PROTEIN  Length:65
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:65
                                    14        24        34        44        54        64     
             HFQ_PSEAE    5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVR 69
               SCOP domains d1u1tc_ C: Pleiotropic translational regulator Hfq                SCOP domains
               CATH domains 1u1tC00 C:5-69  [code=2.30.30.100, no name defined]               CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee....eeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  1u1t C  5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVR 69
                                    14        24        34        44        54        64     


Chain D from PDB  Type:PROTEIN  Length:66
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:66
                                    15        25        35        45        55        65      
             HFQ_PSEAE    6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
               SCOP domains d1u1td_ D: Pleiotropic translational regulator Hfq                 SCOP domains
               CATH domains 1u1tD00 D:6-71  [code=2.30.30.100, no name defined]                CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee....eeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  1u1t D  6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
                                    15        25        35        45        55        65      


Chain E from PDB  Type:PROTEIN  Length:69
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:69
                                    12        22        32        42        52        62         
             HFQ_PSEAE    3 KGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
               SCOP domains d1u1te_ E: Pleiotropic translational regulator Hfq                    SCOP domains
               CATH domains 1u1tE00 E:3-71  [code=2.30.30.100, no name defined]                   CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  1u1t E  3 KGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
                                    12        22        32        42        52        62         


Chain F from PDB  Type:PROTEIN  Length:66
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:66
                                    14        24        34        44        54        64      
             HFQ_PSEAE    5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
               SCOP domains d1u1tf_ F: Pleiotropic translational regulator Hfq                 SCOP domains
               CATH domains 1u1tF00 F:5-70  [code=2.30.30.100, no name defined]                CATH domains
           Pfam domains (1) -----LSM-1u1tF01 F:10-64                                    ------ Pfam domains (1)
           Pfam domains (2) -----LSM-1u1tF02 F:10-64                                    ------ Pfam domains (2)
           Pfam domains (3) -----LSM-1u1tF03 F:10-64                                    ------ Pfam domains (3)
           Pfam domains (4) -----LSM-1u1tF04 F:10-64                                    ------ Pfam domains (4)
           Pfam domains (5) -----LSM-1u1tF05 F:10-64                                    ------ Pfam domains (5)
           Pfam domains (6) -----LSM-1u1tF06 F:10-64                                    ------ Pfam domains (6)
         Sec.struct. author ..hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee....eeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  1u1t F  5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
                                    14        24        34        44        54        64
   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, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: Sm-like (17)
(-)
Family: LSM (13)
(-)
Pseudomonas aeruginosa (2)
1aLSM-1u1tF01F:10-64
1bLSM-1u1tF02F:10-64
1cLSM-1u1tF03F:10-64
1dLSM-1u1tF04F:10-64
1eLSM-1u1tF05F:10-64
1fLSM-1u1tF06F:10-64

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (HFQ_PSEAE | Q9HUM0)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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  1u1t
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 Related Entries

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

UniProtKB/Swiss-Prot
        HFQ_PSEAE | Q9HUM0: 1u1s 3inz 3m4g 3qui 4j5y 4j6w 4j6x 4j6y 4mmk 4mml

(-) Related Entries Specified in the PDB File

1hk9 HFQ PROTEIN FROM E. COLI
1qk1 HFQ PROTEIN FROM S. AUREUS
1qk2 HFQ PROTEIN FROM S. AUREUS IN COMPLEX WITH OLIGO-RNA
1u1s HFQ PROTEIN FROM PSEUDOMONAS AERUGINOSA RELATED ID: MY_001000020.2 RELATED DB: TARGETDB