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(-) Description

Title :  S-SAD STRUCTURE OF DINB-DNA COMPLEX
 
Authors :  J. Kottur, D. T. Nair, T. Weinert, V. Oligeric, M. Wang
Date :  03 Sep 14  (Deposition) - 14 Jan 15  (Release) - 02 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,V,W
Biol. Unit 1:  A,V,W  (1x)
Biol. Unit 2:  B,C,D  (1x)
Keywords :  Nucleotidyl Transferase, Dna Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Weinert, V. Olieric, S. Waltersperger, E. Panepucci, L. Chen, H. Zhang, D. Zhou, J. Rose, A. Ebihara, S. Kuramitsu, D. Li, N. Howe, G. Schnapp, A. Pautsch, K. Bargsten, A. E. Prota, P. Surana, J. Kottur, D. T. Nair, F. Basilico, V. Cecatiello, S. Pasqualato, A. Boland, O. Weichenrieder, B. C. Wang, M. O. Steinmetz, M. Caffrey, M. Wang
Fast Native-Sad Phasing For Routine Macromolecular Structur Determination
Nat. Methods V. 12 131 2015
PubMed-ID: 25506719  |  Reference-DOI: 10.1038/NMETH.3211

(-) Compounds

Molecule 1 - DNA POLYMERASE IV
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41DE3
    Expression System Taxid: 562
    Expression System Vector Type: PGEX6P1
    Fragment: UNP RESIDUES 2-340
    Gene: B0231, DINB, DINP, JW0221
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K12
    Synonym: POL IV
 
Molecule 2 - DNA POLYMERASE IV
    Chains: B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41DE3
    Expression System Taxid: 562
    Expression System Vector Type: PGEX6P1
    Fragment: UNP RESIDUES 2-338
    Gene: B0231, DINB, DINP, JW0221
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K12
    Synonym: POL IV
 
Molecule 3 - DNA
    Chains: V, C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 4 - DNA
    Chains: W
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 5 - DNA
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC OLIGONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDVW
Biological Unit 1 (1x): A   VW
Biological Unit 2 (1x):  BCD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
11FZ2Ligand/Ion5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11FZ1Ligand/Ion5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11FZ1Ligand/Ion5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , MET A:10 , ASP A:104 , 1FZ A:402BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASP A:9 , MET A:10 , ASP A:11 , CYS A:12 , PHE A:13 , PHE A:14 , SER A:43 , THR A:44 , ARG A:50 , SER A:56 , ASP A:104 , GLU A:105 , LYS A:158 , MG A:401 , HOH A:514 , DA V:20 , DC W:54BINDING SITE FOR RESIDUE 1FZ A 402
3AC3SOFTWAREASP B:9 , MET B:10 , ASP B:11 , CYS B:12 , PHE B:13 , PHE B:14 , SER B:43 , THR B:44 , ARG B:50 , SER B:56 , ASP B:104 , LYS B:158 , MG B:402 , DA C:20 , DC D:54BINDING SITE FOR RESIDUE 1FZ B 401
4AC4SOFTWAREASP B:9 , MET B:10 , ASP B:104 , 1FZ B:401BINDING SITE FOR RESIDUE MG B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R8U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:158 -Pro A:159
2Lys B:158 -Pro B:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R8U)

(-) Exons   (0, 0)

(no "Exon" information available for 4R8U)

(-) 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:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhhhhhhhh...eeee........eeeehhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh....eeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh....eee.hhhhhhhhhhh.hhhhh...hhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r8u A   2 SRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLD 341
                                    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


Chain B from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeee.hhhhh..eeeehhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhh..eeeee..eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh......eee.hhhhhhhhhhh.hhhhh...hhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh........eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r8u B   3 RKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLD 340
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        


Chain C from PDB  Type:DNA  Length:17
                                                 
                 4r8u C  18 CTAGGGTCCTAGGACCC  34
                                    27       


Chain D from PDB  Type:DNA  Length:16
                                                
                 4r8u D  39 TAGGGTCCTAGGACCC  54
                                    48      


Chain V from PDB  Type:DNA  Length:17
                                                 
                 4r8u V  18 CTAGGGTCCTAGGACCC  34
                                    27       


Chain W from PDB  Type:DNA  Length:18
                                                  
                 4r8u W  37 TCTAGGGTCCTAGGACCC  54
                                    46
   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 4R8U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R8U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R8U)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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        DPO4_ECOLI | Q47155: 1ok7 1unn 4ir1 4ir9 4irc 4ird 4irk 4q43 4q44 4q45 5c5j

(-) Related Entries Specified in the PDB File

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