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(-) Description

Title :  CRYSTAL STRUCTURE OF PIF1 HELICASE FROM BACTEROIDES IN COMPLEX WITH ADP-ALF3 AND SSDNA
 
Authors :  W. -F. Chen, Y. -X. Dai, X. -L. Duan, N. -N. Liu, W. Shi, M. Li, S. -X. Dou, N. Y. -H. Dong, S. Rety, X. -G. Xi
Date :  12 Jan 16  (Deposition) - 03 Feb 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.19
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Hydrolase, Sf1B, G Quadruplex, Sh3 Domain, Conformational Change (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. -F. Chen, Y. -X. Dai, X. -L. Duan, N. -N. Liu, W. Shi, N. Li, M. Li, S. -X. Dou, Y. -H. Dong, S. Rety, X. -G. Xi
Crystal Structures Of The Bspif1 Helicase Reveal That A Major Movement Of The 2B Sh3 Domain Is Required For Dna Unwinding
Nucleic Acids Res. V. 44 2949 2016
PubMed-ID: 26809678  |  Reference-DOI: 10.1093/NAR/GKW033

(-) Compounds

Molecule 1 - TPR DOMAIN PROTEIN
    Chains: A
    EC Number: 3.6.4.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET15B-SUMO
    Expression System Vector Type: PLASMID
    Organism Scientific: BACTEROIDES
    Organism Taxid: 457390
    Strain: SP. 3_1_23
    Synonym: HELICASE
 
Molecule 2 - 5'-D(*TP*TP*TP*TP*TP*TP)-3'
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AF31Ligand/IonALUMINUM FLUORIDE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:4 , ILE A:5 , LYS A:29 , ALA A:30 , GLY A:31 , SER A:32 , GLY A:33 , LYS A:34 , THR A:35 , THR A:36 , PHE A:187 , ARG A:188 , THR A:367 , ARG A:392 , AF3 A:1433 , MG A:1434BINDING SITE FOR RESIDUE ADP A1432
2AC2SOFTWAREALA A:30 , GLY A:31 , LYS A:34 , THR A:35 , GLU A:106 , GLN A:145 , ARG A:188 , GLY A:365 , ARG A:390 , ADP A:1432 , MG A:1434BINDING SITE FOR RESIDUE AF3 A1433
3AC3SOFTWARETHR A:35 , GLU A:106 , GLY A:365 , ADP A:1432 , AF3 A:1433BINDING SITE FOR RESIDUE MG A1434

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:149 -Thr A:150
2Ser A:224 -Ser A:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FTE)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh......eeeee....hhhhhhhhhh.......eeee.hhhhhhhhh.eehhhhh.................hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhh..hhhhhheeeee..........hhhhhhhhhhhh...hhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhh......hhhhhhhhhh............eee.hhhhhhhhhhhhh......eee.eeee...........eee.....eeee.............eeeeeee....eeeee....eeee..eeeeee..eee..eee..eeeeeee..eee....hhhhhh......eeee.......hhhhhhhhh......eee....hhhhh...hhhhhhhhhhhhh..eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fte A   3 DMILTEEMQKIMNLIQDDENNVFVTGKAGSGKTTFLKYLIEKSGKNCIVAAPTGIAAINAGGVTLHSLFGIPFGPITPYDRLENKFSEYKVELLLKMELLIIDEISMVRPDILDTIDRKLRWVYESDEPFGGVQVIMFGDLFQLPPVTKKQEREILSDFYDGFFFFNALVFKRTGFHIVELTKIFRQTEPEFINVLNNIRNYQVTSDELDLLSELKDRKISSSYDNEYIHICTHKADVEKINADKLGEQEIRNYDIVIKDKFPESSIPCDLHLKLRVGARVMSLVNDSLKGYYNGMLGIVTALEDNVITVRMDNGRTIKFERYTWSNTQYTLKDNEIVKEEIGSCTQFPLTLAWAITIHKSQGLTFDKIIIHVSHTFCPGQLYVALSRCRTLEGIVSDAFITKQMIIPEYALIDFERAYKSEGNYYGKRL 432
                                    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       342       352       362       372       382       392       402       412       422       432


Chain D from PDB  Type:DNA  Length:6
                                      
                 5fte D   3 TTTTTT   8
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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 5FTE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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        D7K0H3_9BACE | D7K0H3: 5ftb 5ftc 5ftd 5ftf

(-) Related Entries Specified in the PDB File

5ftb CRYSTAL STRUCTURE OF PIF1 HELICASE FROM BACTEROIDES IN COMPLEX WITH AMPPNP
5ftc CRYSTAL STRUCTURE OF PIF1 HELICASE FROM BACTEROIDES IN COMPLEX WITH ADP
5ftd CRYSTAL STRUCTURE OF PIF1 HELICASE FROM BACTEROIDES APO FORM
5ftf CRYSTAL STRUCTURE OF PIF1 HELICASE FROM BACTEROIDES DOUBLE MUTANT L95C-I339C