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(-) Description

Title :  CRYSTAL STRUCTURE OF DDRB BOUND TO 30B SSDNA
 
Authors :  S. N. Sugiman-Marangos, Y. M. Weiss, M. S. Junop
Date :  19 Nov 13  (Deposition) - 20 May 15  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Keywords :  Single-Stranded Dna Annealing, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Sugiman-Marangos, Y. M. Weiss, M. S. Junop
Mechanism For Accurate, Protein-Assisted Dna Annealing By Deinococcus Radiodurans Ddrb.
Proc. Natl. Acad. Sci. Usa V. 113 4308 2016
PubMed-ID: 27044084  |  Reference-DOI: 10.1073/PNAS.1520847113

(-) Compounds

Molecule 1 - SINGLE-STRANDED DNA-BINDING PROTEIN DDRB
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151/D-TOPO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-144
    Gene: DDRB, DR0070, DR_0070
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Synonym: DNA DAMAGE RESPONSE PROTEIN B
 
Molecule 2 - 5'-D(*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP *TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP)-3'
    Chains: F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:138 , HOH B:369 , HOH B:371 , HOH B:387 , GLU E:86 , HOH E:231BINDING SITE FOR RESIDUE CA B 201
2AC2SOFTWAREGLU A:86 , GLU D:138 , HOH D:304 , HOH D:309 , HOH D:322 , HOH D:335BINDING SITE FOR RESIDUE CA D 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NOE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NOE)

(-) 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:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.hhhhhhhhhhhhhhh...........eeehhhhh...hhhhhh.eee...eeee..eeeeeeee..ee....ee..eeeeeee.....hhhhhee.hhh.eeeeeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4noe A   1 MLQIEFITDLGARVTVNVEHESRLLDVQRHYGRLGWTSGEIPSGGYQFPIENEADFDWSLIGARKWKEELVIHRGHAYRRRELEAVDSRKLKLPAAIKYSRGAKVSDPQHVREKADGDIEYVSLAIFRGGKRQERYAVP 143
                                    10        20        30        40        50        60      ||74        84        94       104       114       124       134         
                                                                                             67|                                                                       
                                                                                              72                                                                       


Chain B from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.hhhhhhhhhhhhhh............eeehhhhh...hhhhhh.ee..eeee..eeeeeeee.........eeeeeee.....hhhhheeehhheeeeeeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4noe B   1 MLQIEFITDLGARVTVNVEHESRLLDVQRHYGRLGWTSGEIPSGGYQFPIENEADFDWSLIGARKWELVIHRGHAYRRRELEAVDLKLPAAIKYSRGAKVSDPQHVREKADGDIEYVSLAIFRGGKRQERYAVP 143
                                    10        20        30        40        50        60     || 76        86    ||  99       109       119       129       139    
                                                                                            66|                91|                                                
                                                                                             73                 95                                                


Chain C from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeeeee.hhhhhhhhhhhhhh............eeehhhhh...hhhhhh.ee..eeee..eeeeeeee........eeeeeee.....hhhhhee.hhh.eeeeeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4noe C   0 TMLQIEFITDLGARVTVNVEHESRLLDVQRHYGRLGWTSGEIPSGGYQFPIENEADFDWSLIGARKWELVIHRGHAYRRRELEAVDKLPAAIKYSRGAKVSDPQHVREKADGDIEYVSLAIFRGGKRQERYAVP 143
                                     9        19        29        39        49        59      ||75        85     || 99       109       119       129       139    
                                                                                             66|                91|                                               
                                                                                              73                 96                                               


Chain D from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....eeeeee.hhhhhhhhhhhhhh............eeehhhhh...hhhhhh.ee..eeee..eeeeeeee......eeeeeee.....hhhhheee...eeeeeeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4noe D  -1 FTMLQIEFITDLGARVTVNVEHESRLLDVQRHYGRLGWTSGEIPSGGYQFPIENEADFDWSLIGARKWELVIHRGHAYRRRELEAVLPAAIKYSRGAKVSDPQHVREKADGDIEYVSLAIFRGGKRQERYAVP 143
                                     8        18        28        38        48        58       |74        84     ||100       110       120       130       140   
                                                                                              66|               90|                                              
                                                                                               73                97                                              


Chain E from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....eeeeee.hhhhhhhhhhhhhhh...........eeehhhhh...hhhhhh.eeee.....eeeee..eeeeeeee.........eeeeeee.....hhhhhee.hhh.eeeeeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4noe E  -1 FTMLQIEFITDLGARVTVNVEHESRLLDVQRHYGRLGWTSGEIPSGGYQFPIENEADFDWSLIGARKWKSPEGEELVIHRGHAYRRRELEAVDLKLPAAIKYSRGAKVSDPQHVREKADGDIEYVSLAIFRGGKRQERYAVP 143
                                     8        18        28        38        48        58        68        78        88  ||   101       111       121       131       141  
                                                                                                                       91|                                                
                                                                                                                        95                                                


Chain F from PDB  Type:DNA  Length:30
                                                              
                 4noe F   1 TTGCGCTTGCGCTTGCGCTTGCGCTTGCGC  30
                                    10        20        30
   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 4NOE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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