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(-) Description

Title :  CRYSTAL STRUCTURE OF HFQ FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH CTP
 
Authors :  A. D. Nikulin, V. Murina, N. Lekontseva
Date :  12 Feb 13  (Deposition) - 31 Jul 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Lsm, Rna Binding Protein, Rna Chaperone, Srna, Mrna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Murina, N. Lekontseva, A. Nikulin
Hfq Binds Ribonucleotides In Three Different Rna-Binding Sites.
Acta Crystallogr. , Sect. D V. 69 1504 2013
PubMed-ID: 23897473  |  Reference-DOI: 10.1107/S090744491301010X

(-) Compounds

Molecule 1 - PROTEIN HFQ
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HFQ, PA4944
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 25)

Asymmetric/Biological Unit (7, 25)
No.NameCountTypeFull Name
1C4Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2CDP1Ligand/IonCYTIDINE-5'-DIPHOSPHATE
3CL2Ligand/IonCHLORIDE ION
4CTP6Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
5MG8Ligand/IonMAGNESIUM ION
6NA3Ligand/IonSODIUM ION
7P6G1Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:25 , GLY A:29 , LYS A:31 , THR A:61 , HOH A:203 , HOH A:221 , HOH A:234 , HOH A:244 , HOH A:245 , ARG C:69 , ASN E:28 , ILE E:30BINDING SITE FOR RESIDUE CTP A 101
02AC2SOFTWAREHIS A:5 , GLN A:8 , GLN A:41 , PHE A:42 , LYS A:56 , HOH A:233 , HOH A:240 , HOH A:250 , HOH A:260 , CTP B:101 , HOH B:236 , PHE E:42 , HIS E:57 , C E:101 , MG E:104 , MG E:105 , HOH E:229BINDING SITE FOR RESIDUE C A 102
03AC3SOFTWAREASP A:9 , PHE A:39 , ASP A:40 , LYS A:56BINDING SITE FOR RESIDUE MG A 103
04AC4SOFTWAREP6G D:103 , HOH D:227BINDING SITE FOR RESIDUE NA A 104
05AC5SOFTWAREPHE A:42 , TYR A:55 , HIS A:57 , C A:102 , HOH A:240 , HOH A:260 , HIS B:5 , GLN B:8 , GLN B:41 , PHE B:42 , LYS B:56 , HIS B:57 , MG B:102 , HOH B:206 , HOH B:220 , HOH B:221 , HOH B:222 , HOH B:236 , HOH B:237 , HOH B:238 , MG C:103 , MG C:104 , C D:101 , MG D:105 , HOH D:208 , C E:101 , MG E:105 , HOH E:229 , CDP F:101 , HOH F:228BINDING SITE FOR RESIDUE CTP B 101
06AC6SOFTWARECTP B:101 , HOH B:222 , HOH B:236 , C D:101 , HOH D:226BINDING SITE FOR RESIDUE MG B 102
07AC7SOFTWARETYR C:25 , GLY C:29 , LYS C:31 , SER C:60 , THR C:61 , HOH C:202 , HOH C:230 , HOH C:236 , HOH C:243 , ASN F:28 , ILE F:30 , HOH F:202BINDING SITE FOR RESIDUE CTP C 101
08AC8SOFTWAREHIS C:5 , GLN C:8 , GLN C:41 , PHE C:42 , LYS C:56 , MG C:103 , MG C:104 , HOH C:224 , C E:101 , PHE F:42 , TYR F:55 , HIS F:57 , CDP F:101 , NA F:105BINDING SITE FOR RESIDUE C C 102
09AC9SOFTWARECTP B:101 , C C:102 , MG C:104 , C E:101 , CDP F:101BINDING SITE FOR RESIDUE MG C 103
10BC1SOFTWAREHOH A:260 , CTP B:101 , HOH B:237 , C C:102 , MG C:103 , C D:101 , CDP F:101 , NA F:105BINDING SITE FOR RESIDUE MG C 104
11BC2SOFTWAREPHE B:42 , HIS B:57 , CTP B:101 , MG B:102 , HOH B:237 , MG C:104 , HIS D:5 , GLN D:8 , GLN D:41 , PHE D:42 , LYS D:56 , HIS D:57 , MG D:104 , MG D:105 , HOH D:226 , CDP F:101 , NA F:105BINDING SITE FOR RESIDUE C D 101
12BC3SOFTWARELEU B:26 , ASN B:28 , ILE B:30 , HOH B:203 , GLN C:35 , ASN C:48 , TYR D:25 , GLY D:29 , LYS D:31 , SER D:60 , THR D:61 , HOH D:202 , HOH D:219 , HOH D:221BINDING SITE FOR RESIDUE CTP D 102
13BC4SOFTWARENA A:104 , VAL B:27 , ARG C:66 , VAL D:27 , HOH D:227 , VAL F:27BINDING SITE FOR RESIDUE P6G D 103
14BC5SOFTWAREPHE D:42 , LYS D:56 , HIS D:57 , C D:101 , CDP F:101BINDING SITE FOR RESIDUE MG D 104
15BC6SOFTWARECTP B:101 , HOH B:220 , C D:101 , CDP F:101BINDING SITE FOR RESIDUE MG D 105
16BC7SOFTWAREC A:102 , HOH A:233 , HOH A:260 , CTP B:101 , PHE C:42 , TYR C:55 , HIS C:57 , C C:102 , MG C:103 , HOH C:207 , GLY E:4 , GLN E:8 , GLN E:41 , PHE E:42 , LYS E:56 , HIS E:57 , MG E:104 , MG E:105 , HOH E:204 , HOH E:229BINDING SITE FOR RESIDUE C E 101
17BC8SOFTWAREASN C:28 , ILE C:30 , HOH C:204 , TYR E:25 , GLY E:29 , LYS E:31 , SER E:60 , THR E:61 , HOH E:201 , HOH E:209 , HOH E:217 , HOH E:227 , HOH E:230 , HOH E:237BINDING SITE FOR RESIDUE CTP E 102
18BC9SOFTWARELYS E:31 , HOH E:230BINDING SITE FOR RESIDUE CL E 103
19CC1SOFTWAREC A:102 , HOH A:233 , HOH A:260 , C E:101BINDING SITE FOR RESIDUE MG E 104
20CC2SOFTWAREC A:102 , HOH A:249 , CTP B:101 , HIS E:57 , C E:101 , HOH E:229BINDING SITE FOR RESIDUE MG E 105
21CC3SOFTWARECTP B:101 , HOH B:238 , HIS C:57 , C C:102 , MG C:103 , MG C:104 , HOH C:224 , PHE D:42 , TYR D:55 , HIS D:57 , C D:101 , MG D:104 , MG D:105 , GLY F:4 , GLN F:8 , GLN F:41 , PHE F:42 , LYS F:56 , HIS F:57 , NA F:105 , HOH F:212 , HOH F:228 , HOH F:235BINDING SITE FOR RESIDUE CDP F 101
22CC4SOFTWAREARG C:19 , ASN D:28 , ILE D:30 , TYR F:25 , GLY F:29 , THR F:61 , HOH F:204 , HOH F:213 , HOH F:233 , HOH F:241 , HOH F:249BINDING SITE FOR RESIDUE CTP F 102
23CC5SOFTWARESER D:51 , HOH D:218 , PRO F:67 , VAL F:68BINDING SITE FOR RESIDUE CL F 103
24CC6SOFTWAREGLU E:18 , GLU F:18 , VAL F:68 , ARG F:69BINDING SITE FOR RESIDUE NA F 104
25CC7SOFTWAREHOH B:237 , C C:102 , MG C:104 , HOH C:224 , C D:101 , CDP F:101BINDING SITE FOR RESIDUE NA F 105

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J6W)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly E:4 -His E:5
2Gly F:4 -His F:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J6W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J6W)

(-) Exons   (0, 0)

(no "Exon" information available for 4J6W)

(-) 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:67
                                                                                                  
               SCOP domains d4j6wa_ A: Pleiotropic translational regulator Hfq                  SCOP domains
               CATH domains ------------------------------------------------------------------- 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
                  4j6w A  5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
                                    14        24        34        44        54        64       


Chain B from PDB  Type:PROTEIN  Length:66
                                                                                                 
               SCOP domains d4j6wb_ B: Pleiotropic translational regulator Hfq                 SCOP domains
               CATH domains ------------------------------------------------------------------ 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
                  4j6w B  5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
                                    14        24        34        44        54        64      


Chain C from PDB  Type:PROTEIN  Length:66
                                                                                                 
               SCOP domains d4j6wc_ C: Pleiotropic translational regulator Hfq                 SCOP domains
               CATH domains ------------------------------------------------------------------ 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
                  4j6w C  5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
                                    14        24        34        44        54        64      


Chain D from PDB  Type:PROTEIN  Length:65
                                                                                                
               SCOP domains d4j6wd_ D: Pleiotropic translational regulator Hfq                SCOP domains
               CATH domains ----------------------------------------------------------------- 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
                  4j6w D  5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVR 69
                                    14        24        34        44        54        64     


Chain E from PDB  Type:PROTEIN  Length:66
                                                                                                 
               SCOP domains d4j6we_ E: Pleiotropic translational regulator Hfq                 SCOP domains
               CATH domains ------------------------------------------------------------------ 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
                  4j6w E  4 GHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVR 69
                                    13        23        33        43        53        63      


Chain F from PDB  Type:PROTEIN  Length:69
                                                                                                    
               SCOP domains d4j6wf_ F: Pleiotropic translational regulator Hfq                    SCOP domains
               CATH domains --------------------------------------------------------------------- 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
                  4j6w F  4 GHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLPS 72
                                    13        23        33        43        53        63
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  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  (0, 0)

(no "CATH Domain" information available for 4J6W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J6W)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  4j6w
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 Related Entries

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

UniProtKB/Swiss-Prot
        HFQ_PSEAE | Q9HUM0: 1u1s 1u1t 3inz 3m4g 3qui 4j5y 4j6x 4j6y 4mmk 4mml

(-) Related Entries Specified in the PDB File

1u1s WILD-TYPE PROTEIN
1u1t WILD-TYPE PROTEIN
3qui HFQ FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH ADPNP
4j5y HFQ FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH ATP
4j6x HFQ FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH UTP
4j6y HFQ FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH GTP