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(-) Description

Title :  CRYSTAL STRUCTURE OF APETHERMO-DBP-RP2 BOUND TO SSDNA DT10
 
Authors :  H. Gahlei, H. Von Moeller, D. Eppers, B. Loll, M. C. Wahl
Date :  07 Mar 14  (Deposition) - 30 Apr 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,L,X,Z
Biol. Unit 1:  A,B,C,D,E,L  (1x)
Biol. Unit 2:  F,G,H,I,X,Z  (1x)
Keywords :  Ssdna Binding Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ghalei, H. V. Moeller, D. Eppers, D. Sohmen, D. N. Wilson, B. Loll, M. C. Wahl
Entrapment Of Dna In An Intersubunit Tunnel System Of A Single-Stranded Dna-Binding Protein.
Nucleic Acids Res. V. 42 6698 2014
PubMed-ID: 24744237  |  Reference-DOI: 10.1093/NAR/GKU259

(-) Compounds

Molecule 1 - SSDNA BINDING PROTEIN
    Chains: A, B, C, D, F, G, H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-M11
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APE_1866.1
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
 
Molecule 2 - POLYDEOXYRIBONUCLEOTIDE
    Chains: L, E, X, Z
    Engineered: YES
    Other Details: SSDNA OLIGONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHILXZ
Biological Unit 1 (1x): ABCDE    L  
Biological Unit 2 (1x):      FGHI XZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:19 , PHE A:23 , ARG B:204 , ARG B:208 , DT L:5 , DT L:6BINDING SITE FOR RESIDUE PO4 B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Glu A:165 -Pro A:166
2Glu B:165 -Pro B:166
3Glu C:165 -Pro C:166
4Glu D:165 -Pro D:166
5Glu F:165 -Pro F:166
6Glu G:165 -Pro G:166
7Glu H:165 -Pro H:166
8Glu I:165 -Pro I:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PSO)

(-) 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee....eeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee..eeeeeeeeee....eeeeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pso A   0 MLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAMAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRIMYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLV 217
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209        


Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee....eeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee..eeeeeeeeee...eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pso B  -1 AMLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAMAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRIMYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLVK 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218


Chain C from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee....eeeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee..eeeeeeeeee...eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pso C  -1 AMLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAMAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRIMYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLVK 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218


Chain D from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee....eeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee..eeeeeeeeee....eeeeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pso D  -1 AMLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAMAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRIMYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLV 217
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208         


Chain E from PDB  Type:DNA  Length:7
                                       
                 4pso E  -3 TTTTTTT   3


Chain F from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee....eeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee..eeeeeeeeee...eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pso F   0 MLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAMAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRIMYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLVK 218
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         


Chain G from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...ee..hhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee....eeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee..eeeeeeeeee...eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pso G   0 MLPTLRTGLVIAAGYADKVRVLFAQLRDAIKSGELSNKDVAMAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRIMYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLV 217
                                     9        19|       30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
                                              19|                                                                                                                                                                                                    
                                               21                                                                                                                                                                                                    


Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee....eeeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee..eeeeeeeeee...eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pso H  -1 AMLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAMAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRIMYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLVK 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218


Chain I from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee....eeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee..eeeeeeeeee...eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pso I  -2 GAMLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAMAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRIMYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLVK 218
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 


Chain L from PDB  Type:DNA  Length:10
                                          
                 4pso L   1 TTTTTTTTTT  10
                                    10


Chain X from PDB  Type:DNA  Length:4
                                    
                 4pso X   7 TTTT  10


Chain Z from PDB  Type:DNA  Length:4
                                    
                 4pso Z  11 TTTT  14
   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 4PSO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  4pso
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  Q9YAS7_AERPE | Q9YAS7
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        Q9YAS7_AERPE | Q9YAS7: 4psn

(-) Related Entries Specified in the PDB File

4psl 4psm 4psn