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(-) Description

Title :  STRUCTURE OF RECJ COMPLEXED WITH DNA AND SSB-CT
 
Authors :  Y. Zhao, Y. Hua, K. Cheng
Date :  04 Dec 15  (Deposition) - 15 Jun 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Recf Pathway, Dna End Resection, Two-Metal-Ion Catalysis, Single- Strand-Dna, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Cheng, H. Xu, X. Chen, L. Wang, B. Tian, Y. Zhao, Y. Hua
Structural Basis For Dna 5 -End Resection By Recj
Elife V. 5 14294 2016
PubMed-ID: 27058167  |  Reference-DOI: 10.7554/ELIFE.14294

(-) Compounds

Molecule 1 - SINGLE-STRANDED-DNA-SPECIFIC EXONUCLEASE
    Atcc: ATCC13939
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET28
    Expression System Strain: BL21(DE3) ROSSETTA
    Expression System Taxid: 562
    Gene: RECJ
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
 
Molecule 2 - DNA (5'-D(*CP*TP*GP*AP*TP*GP*GP*CP*A)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - ALA-ASP-LEU-PRO-PHE
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:438 , VAL A:439 , TRP A:663 , HOH A:942binding site for residue SO4 A 801
2AC2SOFTWAREARG A:109 , GLY A:348 , SER A:371 , ARG A:373 , HOH A:918 , HOH A:997 , DC C:1binding site for residue SO4 A 802
3AC3SOFTWARESER A:606 , ARG A:609binding site for residue SO4 A 803
4AC4SOFTWAREASP A:79 , ASP A:81 , ASP A:135 , DT C:2binding site for residue MN A 804
5AC5SOFTWAREASP A:83 , ASP A:135 , HIS A:159 , ASP A:223 , DT C:2binding site for residue MN A 805

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F56)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:454 -Pro A:455

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F56)

(-) Exons   (0, 0)

(no "Exon" information available for 5F56)

(-) 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:703
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhh.eeee......hhhhhhhhhhh..eeeee............eeehhhhh..........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhh..eeeee..eeeee.....hhhhhhhhhhh.eeeeee...eeeeee...hhhhhhhhhhhhhhh......eeee.ee.hhhhhhhhhhhhhhhhh..........eeeeeeeeeeeee.....eeeeee..eeeee........eeeeeeeeeeee......eeeeeeeeeee....ee.............hhhhhhhhhhh..eee.hhhhhhhhhhhh...............eeee....hhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f56 A   2 SRPAHWLLAPPASRDALLATMREWQVSPPVAQVLCGRDLRTELLALPLELTPNPALREAARHIVAAVREGKRIRIHGDYDADGVSATATLVLGLRAIGANVHGFIPHRLNEGYGIHPDRVPEHAAAADLVVTVDCGVSNLDEVKSLLATGTEVVVTDHHAPGENFPECLVVHPHLTPDYDPDRHNLTGAGVAYHLLWAVYEELGRPEPRALLPLATLGTVADVAPLLGENRALVRAGLAEMARTELPGLRALMNEKRVRQPTARDVAFILAPRINAAGRMGEADRALELLTTPSDHEAKSLAAYLEIRNQERRKIQDDMFAQALQLADPNDPALVLTHDDWHAGVMGIVASKLVETFNRPVYIVAQGKGSVRSTPGISAVQGLRESRDLLGRFGGHPGAAGFSLDPQNFGALRERIHGYVRQFPTPVPAVRLDAPLPVAALTPELLSELSILEPFGEGNPRPLWHLRGPLTDTRLVGKQGDVLQFRFGGVKGMKYSERDDAAGERDVAAELALNEWKGRTSLELHAAALRPLAPLALAGTEEGLPTLPRLNPREAMTFLKTGAAAYAEQGVATYLRDNVPGLTLLDTNAPHPGGDLILYGLPPESALRRWLHEAQEQGGRVAFALGPKTLAELDAALTLAKLLPDSHTEAAQEAAADAYRSWQWAHHYRVLNDAGWSASVYAMLGLPVPAALPKAAEALALAA 704
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701   


Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5f56 B 297 ADLPF 301


Chain C from PDB  Type:DNA  Length:9
                                         
                 5f56 C   1 CTGATGGCA   9
   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 5F56)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F56)

(-) Gene Ontology  (10, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:454 - Pro A:455   [ RasMol ]  
 

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  5f56
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 Related Entries

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

UniProtKB/TrEMBL
        D0EM60_DEIRD | D0EM60: 5f54 5f55

(-) Related Entries Specified in the PDB File

5f54 5f55