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(-) Description

Title :  CRYSTAL STRUCTURE OF XERH SITE-SPECIFIC RECOMBINASE BOUND TO PALINDROMIC DIFH SUBSTRATE: POST-CLEAVAGE COMPLEX
 
Authors :  A. Bebel, O. Barabas
Date :  25 Apr 16  (Deposition) - 28 Dec 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Keywords :  Xer, Tyrosine Recombinase, Site-Specific Recombinase, Chromosome Dimer Resolution, Cell Cycle, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bebel, E. Karaca, B. Kumar, W. M. Stark, O. Barabas
Structural Snapshots Of Xer Recombination Reveal Activation By Synaptic Complex Remodeling And Dna Bending.
Elife V. 5 2016
PubMed-ID: 28009253  |  Reference-DOI: 10.7554/ELIFE.19706

(-) Compounds

Molecule 1 - TYROSINE RECOMBINASE XERH
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETM-28
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: XERH, HP_0675
    Organism Scientific: HELICOBACTER PYLORI (STRAIN ATCC 700392 / 26695)
    Organism Taxid: 85962
    Strain: ATCC 700392 / 26695
 
Molecule 2 - DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')
    Chains: C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HELICOBACTER PYLORI 26695
    Organism Taxid: 85962
 
Molecule 3 - DNA (5'- D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')
    Chains: D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HELICOBACTER PYLORI 26695
    Organism Taxid: 85962

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL9Ligand/IonGLYCEROL
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL18Ligand/IonGLYCEROL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:58 , ASP B:10 , GLU B:13binding site for residue GOL A 401
02AC2SOFTWAREGLU A:304 , LYS A:305 , DC F:23 , DA F:24binding site for residue GOL A 402
03AC3SOFTWARELEU A:266 , TYR A:267 , GLN A:278binding site for residue GOL A 403
04AC4SOFTWAREHIS A:324 , HIS B:324binding site for residue GOL A 404
05AC5SOFTWARELYS A:102 , ASP A:145 , LYS A:149 , TYR A:151binding site for residue GOL A 405
06AC6SOFTWAREALA A:336 , SER A:337 , THR A:340 , DC E:13binding site for residue CL A 406
07AC7SOFTWAREGLY A:118 , ASN B:32 , VAL B:35 , GLN B:38binding site for residue GOL B 401
08AC8SOFTWAREGLU B:304 , LYS B:305 , DA D:24binding site for residue GOL B 402
09AC9SOFTWAREGLU B:6 , LEU B:8binding site for residue GOL B 403
10AD1SOFTWAREARG A:342 , HIS B:324 , LEU B:326 , ILE B:327 , HOH B:508binding site for residue GOL B 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JJV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JJV)

(-) 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:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh................................hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhh.hhh.eeee..eeeeeee.....eeeeeee...hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jjv A   1 MKHPLEELKDPTENLLLWIGRFLRYKCTSLSNSQVKDQNKVFECLNELNQACSSSQLEKVCKKARNAGLLGINTYALPLLKFHEYFSKAFNSLKNIDEVMLAEFLSVYTGGLSLATKKNYRIALLGLFSYIDKQNQDENEKSYIYNITLKNISGVNQSAGNKLPTHLNNEELEKFLESIDKIEMSAKVRARNRLLIKIIVFTGMRSNEALQLKIKDFTLENGCYTILIKGKGDKYRAVMLKAFHIESLLKEWLIERELYPVKNDLLFCNQKGSALTQAYLYKQVERIINFAGLRREKNGAHMLRHSFATLLYQKRHDLILVQEALGHASLNTSRIYTHFDKQRLEEAASIWEE 361
                                    10        20        30        40        50        60        70        80        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358   
                                                                                                                   89|                                                                                                                                                                                                                                                                       
                                                                                                                    98                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhh.hhh.eeee..eeeeeee.hhh.eeeeeee...hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jjv B   0 SMKHPLEELKDPTENLLLWIGRFLRYKCTSLSNSQVKDQNKVFECLNELNQACSSSQLEKVCKKARNAGLLGINTYALPLLKFHEYFSKARLITERLAFNSLKNIDEVMLAEFLSVYTGGLSLATKKNYRIALLGLFSYIDKQNQDENEKSYIYNITLKNISGNKLPTHLNNEELEKFLESIDKIEMSAKVRARNRLLIKIIVFTGMRSNEALQLKIKDFTLENGCYTILIKGKGDKYRAVMLKAFHIESLLKEWLIERELYPVKNDLLFCNQKGSALTQAYLYKQVERIINFAGLRREKNGAHMLRHSFATLLYQKRHDLILVQEALGHASLNTSRIYTHFDKQRLEEAASIWEE 361
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 ||    175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355      
                                                                                                                                                                                           161|                                                                                                                                                                                                 
                                                                                                                                                                                            168                                                                                                                                                                                                 


Chain C from PDB  Type:DNA  Length:13
                                             
                 5jjv C   1 TAGTTATGAAAAC  13
                                    10   


Chain D from PDB  Type:DNA  Length:17
                                                 
                 5jjv D  14 TGCAGTTTTCATAACTA  30
                                    23       


Chain E from PDB  Type:DNA  Length:13
                                             
                 5jjv E   1 TAGTTATGAAAAC  13
                                    10   


Chain F from PDB  Type:DNA  Length:17
                                                 
                 5jjv F  14 TGCAGTTTTCATAACTA  30
                                    23
   Legend:   → Mismatch (orange background)
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  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 5JJV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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  5jjv
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        XERH_HELPY | O25386: 5jk0

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