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(-) Description

Title :  CRYSTAL STRUCTURE OF KLEBSIELLA PNEUMONIAE PMRA IN COMPLEX WITH PMRA BOX DNA
 
Authors :  C. D. Hsiao, T. H. Weng, Y. C. Li
Date :  30 Dec 14  (Deposition) - 11 Nov 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Two-Component System, Response Regulator, Pmra, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. C. Lou, T. H. Weng, Y. C. Li, Y. F. Kao, W. F. Lin, H. L. Peng, S. H. Chou, C. D. Hsiao, C. Chen
Structure And Dynamics Of Polymyxin-Resistance-Associated Response Regulator Pmra In Complex With Promoter Dna.
Nat Commun V. 6 8838 2015
PubMed-ID: 26564787  |  Reference-DOI: 10.1038/NCOMMS9838

(-) Compounds

Molecule 1 - DNA-BINDING TRANSCRIPTIONAL REGULATOR BASR
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: N559_3529
    Mutation: YES
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 1380908
    Strain: JM45
 
Molecule 2 - DNA (25-MER)
    Chains: C, G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: LEADING STRAND
    Synthetic: YES
 
Molecule 3 - DNA (25-MER)
    Chains: D, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: LAGGING STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1BEF4Ligand/IonBERYLLIUM TRIFLUORIDE ION
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BEF2Ligand/IonBERYLLIUM TRIFLUORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1BEF2Ligand/IonBERYLLIUM TRIFLUORIDE ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:51 , GLY A:53 , THR A:79 , ALA A:80 , LYS A:101 , MG A:302BINDING SITE FOR RESIDUE BEF A 301
2AC2SOFTWAREASP A:8 , ASP A:51 , GLY A:53 , BEF A:301BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWAREASP B:51 , GLY B:53 , THR B:79 , ALA B:80 , LYS B:101 , MG B:302BINDING SITE FOR RESIDUE BEF B 301
4AC4SOFTWAREGLU B:7 , ASP B:8 , ASP B:51 , GLY B:53 , BEF B:301BINDING SITE FOR RESIDUE MG B 302
5AC5SOFTWAREASP E:51 , GLY E:53 , THR E:79 , ALA E:80 , LYS E:101 , MG E:302BINDING SITE FOR RESIDUE BEF E 301
6AC6SOFTWAREGLU E:7 , ASP E:8 , ASP E:51 , GLY E:53 , BEF E:301BINDING SITE FOR RESIDUE MG E 302
7AC7SOFTWAREASP F:51 , GLY F:53 , THR F:79 , ALA F:80 , LYS F:101 , MG F:302BINDING SITE FOR RESIDUE BEF F 301
8AC8SOFTWAREGLU F:7 , ASP F:8 , ASP F:51 , GLY F:53 , BEF F:301BINDING SITE FOR RESIDUE MG F 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S04)

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Thr A:93 -Gly A:94
2Lys A:101 -Pro A:102
3Lys A:203 -Ser A:204
4Lys B:101 -Pro B:102
5Lys B:203 -Ser B:204
6Thr E:93 -Gly E:94
7Lys E:101 -Pro E:102
8Asn E:125 -Glu E:126
9Lys E:203 -Ser E:204
10Lys F:101 -Pro F:102
11Ser F:180 -Gly F:181
12Gly F:181 -Asp F:182
13Ile F:201 -Gly F:202
14Lys F:203 -Ser F:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S04)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S04)

(-) Exons   (0, 0)

(no "Exon" information available for 4S04)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhhh.....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh....eeee..eeee....eeee..ee...hhhhhhhhhhhhhh....eehhhhhhhhh........hhhhhhhhhhhhhhh...eeee...eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s04 A   1 MKILVIEDDALLLQGLILAMQSEGYVCDGVSTAHEAALSLASNHYSLIVLDLGLPDEDGLHFLSRMRREKMTQPVLILTARDTLEDRISGLDTGADDYLVKPFALEELNARIRALLRRHNNQGDNEISVGNLRLNVTRRLVWLGETALDLTPKEYALLSRLMMKAGSPVHREILYNDIYSGDNEPATNTLEVHIHNLREKIGKSRIRTVRGFGYMLANN 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhhh.....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhh...........eee......eee..eee..hhhhhhhhhhhhhh....eehhhhhhhh.........hhhhhhhhhhhhhh....eee....eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s04 B   1 MKILVIEDDALLLQGLILAMQSEGYVCDGVSTAHEAALSLASNHYSLIVLDLGLPDEDGLHFLSRMRREKMTQPVLILTARDTLEDRISGLDTGADDYLVKPFALEELNARIRALLRRHNNQGDNEISVGNLRLNVTRRLVWLGETALDLTPKEYALLSRLMMKAGSPVHREILYNDIYSGDNEPATNTLEVHIHNLREKIGKSRIRTVRGFGYMLANN 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain C from PDB  Type:DNA  Length:25
                                                         
                 4s04 C   1 ATTTCTTAATATTATCCTAAGCAAG  25
                                    10        20     


Chain D from PDB  Type:DNA  Length:25
                                                         
                 4s04 D   1 TTGCTTAGGATAATATTAAGAAATC  25
                                    10        20     


Chain E from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhhh.....eeeee...hhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhh......eee..eeee....eeee..ee...hhhhhhhhhhhhhh.....hhhhhhhhhh.........hhhhhhhhhhhhhh...eee.....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s04 E   1 MKILVIEDDALLLQGLILAMQSEGYVCDGVSTAHEAALSLASNHYSLIVLDLGLPDEDGLHFLSRMRREKMTQPVLILTARDTLEDRISGLDTGADDYLVKPFALEELNARIRALLRRHNNQGDNEISVGNLRLNVTRRLVWLGETALDLTPKEYALLSRLMMKAGSPVHREILYNDIYSGDNEPATNTLEVHIHNLREKIGKSRIRTVRGFGYMLANN 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain F from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhhh.....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhh.....eeee..eeee....eeee..ee...hhhhhhhhhhhhhh....eehhhhhhhhh........hhhhhhhhhhhhhhh...eeee...eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s04 F   1 MKILVIEDDALLLQGLILAMQSEGYVCDGVSTAHEAALSLASNHYSLIVLDLGLPDEDGLHFLSRMRREKMTQPVLILTARDTLEDRISGLDTGADDYLVKPFALEELNARIRALLRRHNNQGDNEISVGNLRLNVTRRLVWLGETALDLTPKEYALLSRLMMKAGSPVHREILYNDIYSGDNEPATNTLEVHIHNLREKIGKSRIRTVRGFGYMLANN 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain G from PDB  Type:DNA  Length:25
                                                         
                 4s04 G   1 ATTTCTTAATATTATCCTAAGCAAG  25
                                    10        20     


Chain H from PDB  Type:DNA  Length:25
                                                         
                 4s04 H   1 TTGCTTAGGATAATATTAAGAAATC  25
                                    10        20
   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 4S04)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S04)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S04)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4S04)

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        A0A0R4I965_K | A0A0R4I965: 4s05

(-) Related Entries Specified in the PDB File

4s05