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(-) Description

Title :  STRUCTURE OF PNOB8 PARA BOUND TO NONSPECIFIC DNA
 
Authors :  M. A. Schumacher
Date :  28 Nov 16  (Deposition) - 19 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,C,D,U,W
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A,D  (1x)
Biol. Unit 3:  U,W  (1x)
Biol. Unit 4:  A,B,C,D,U,W  (1x)
Keywords :  Para, Nonspecific Dna Binding, Nucleoid, Segregation, Parb, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zhang, M. A. Schumacher
Structures Of Partition Protein Para With Nonspecific Dna And Parb Effector Reveal Molecular Insights Into Principles Governing Walker-Box Dna Segregation.
Genes Dev. V. 31 481 2017
PubMed-ID: 28373206  |  Reference-DOI: 10.1101/GAD.296319.117

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: B, A, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNOB8
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: SULFOLOBUS SP. NOB8H2
    Organism Taxid: 84600
 
Molecule 2 - DNA (5'- D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*AP*TP*GP*AP*CP*AP*CP*G)- 3')
    Chains: U
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*CP*GP*TP*GP*TP*AP*AP*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)- 3')
    Chains: W
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDUW
Biological Unit 1 (1x):  BC   
Biological Unit 2 (1x): A  D  
Biological Unit 3 (1x):     UW
Biological Unit 4 (1x): ABCDUW

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ANP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ANP-1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1ANP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:14 , VAL B:15 , GLY B:16 , LYS B:17 , THR B:18 , THR B:19 , SER B:45binding site for residue ANP B 401
2AC2SOFTWAREGLY A:14 , VAL A:15 , GLY A:16 , LYS A:17 , THR A:18 , THR A:19binding site for residue ANP A 401
3AC3SOFTWAREGLY C:16 , LYS C:17 , THR C:18 , THR C:19binding site for residue ANP C 401
4AC4SOFTWARELYS D:17 , THR D:18 , THR D:19 , GLN D:43 , SER D:45binding site for residue ANP D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U1J)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr B:197 -Pro B:198
2Tyr B:238 -Pro B:239
3Tyr A:197 -Pro A:198
4Tyr A:238 -Pro A:239
5Tyr C:197 -Pro C:198
6Tyr C:238 -Pro C:239
7Tyr D:197 -Pro D:198
8Tyr D:238 -Pro D:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U1J)

(-) Exons   (0, 0)

(no "Exon" information available for 5U1J)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhh......hhhhhhhh.....eeeeeee..eeeeeeee...hhhhhhhhh.....hhhhhhhh.......eeeeee......hhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhhhhhh............eeeeeee.....hhhhhhhhhhhhhhhhh..hhhhhh............hhhhhh.............hhhhhhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u1j A   2 IAKVITIHNFKGGVGKTTTTAIIAMGLGAMGKRVLLIDFDAQMSLTQIFVREEDRLKILESSHDQDKSAFALLRTMEPARIKFFHEGKGVKFGIDVIPGSYMSIFKLMFEIQSEWNILRMLDLYRDQYDYILIDTAPSDTVTIKPILRASHYLLIPEDGTPEAFTAMRIFLNEALPKYILPRPEGGFYKYPRILGVILTRVRRNSTAILMKHNKILEEELSNSELKDHVIYPPYFGADKDNPEDYILSLSDLIWRDEKRAPISEVFDKLFSKVFTEIPKEVVRRVENDQ 315
                                    11        21        31        41        51        61   ||   73        83        93       103       113|      127       137       147       157       167       177       187       197       207       217       227       237       247       262       272       296       306         
                                                                                          65|                                          113|                                                                                                                                      255|                 281|                   
                                                                                           68                                           118                                                                                                                                       261                  296                   


Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhh....hhhhhhhh.....eeeeeee..eeeeeeee...hhhhhhhh......hhhhhhhh.......eeeee.......hhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhh............eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh............hhhh.ee............hhhhhhhhhh.....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u1j B   2 IAKVITIHNFKGGVGKTTTTAIIAMGLGAMGKRVLLIDFDAQMSLTQIFVREEDRLKILESSHQDKSAFALLRTMEPARIKFFHEGKGVKFGIDVIPGSYMSIFKLMFEIQSEWNILRMLDLYRDQYDYILIDTAPSDTVTIKPILRASHYLLIPEDGTPEAFTAMRIFLNEALPKYILPRPEGGFYKYPRILGVILTRVRRNSTAILMKHNKILEEELSNSELKDHVIYPPYFGADKDNPEDYILSSSDLIWRDEKRAPISEVFDKLFAFFSKVFTEIPKEVVRRVENDQ 315
                                    11        21        31        41        51        61  ||    74        84        94       104       118       128       138       148       158       168       178       188       198       208       218       228       238       248       263       273       294       304       314 
                                                                                         64|                                          113|                                                                                                                                       256|                 282|                     
                                                                                          68                                           118                                                                                                                                        262                  294                     


Chain C from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh....hhhhhhhh.....eeeee......eeeeee...hhhhhhhhh....hhhhhhhhhh.....eeeee.......hhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhhhh............eeeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhh...........hhhhh..............hhhhhhhhhh......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u1j C   2 IAKVITIHNFKGGVGKTTTTAIIAMGLGAMGKRVLLIDFDAQMSLTQIFVREEDRLKILESSHDDKSAFALLRTMEPARIKFFHEGKGVKFGIDVIPGSYMSIFKLMFIQSEWNILRMLDLYRDQYDYILIDTAPSDTVTIKPILRASHYLLIPEDGTPEAFTAMRIFLNEALPKYILPRPEGGFYKYPRILGVILTRVRRNSTAILMKHNKILEEELSNSELKDHVIYPPYFGADKDNPEDYILSSSDLIWRDEKRAPISEVFDKLFFSKVFTEIPKEVVRRVENDQ 315
                                    11        21        31        41        51        61   ||   74        84        94       104       119       129       139       149       159       169       179       189       199       209       219       229       239       249      |264       274       297       307        
                                                                                          65|                                        112|                                                                                                                                       256|                 282|                   
                                                                                           69                                         118                                                                                                                                        262                  296                   


Chain D from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhh....hhhhhhhh.....eeeeeee..eeeeeeee...hhhhhhh.....hhhhhhh........eeeeee......hhhhhhhhh.eeeeee..hhhhhhhhhhhh.hhhhhhh............eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh..................hhhhhhhhh...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u1j D   2 IAKVITIHNFKGGVGKTTTTAIIAMGLGAMGKRVLLIDFDAQMSLTQIFVREEDRLKILESSHQDKSAFALLRTMEPARIKFFHEGKGVKFGIDVIPGSYMSIFKLMFQSEWNILRMLDLYRDQYDYILIDTAPSDTVTIKPILRASHYLLIPEDGTPEAFTAMRIFLNEALPKYILPRPEGGFYKYPRILGVILTRVRRNSTAILMKHNKILEEELSNSELKDHVIYPPYFGADKDNPEDYILSSRKEYLSDLIWRDEKRAPISEVFDKLFSKVFTEIPKEVVRRVENDQ 315
                                    11        21        31        41        51        61  ||    74        84        94       104       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280 ||    304       314 
                                                                                         64|                                         112|                                                                                                                                                                282|                  
                                                                                          68                                          119                                                                                                                                                                 297                  


Chain U from PDB  Type:DNA  Length:21
                                                     
                 5u1j U   1 TGACGCCGGCGTCATGACACG  21
                                    10        20 


Chain W from PDB  Type:DNA  Length:21
                                                     
                 5u1j W   4 CGTGTAATGACGCCGGCGTCA  24
                                    13        23
   Legend:   → Mismatch (orange background)
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  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 5U1J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U1J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U1J)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5U1J)

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        O93708_9CREN | O93708: 5k5z

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5u1g