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(-) Description

Title :  CRYSTAL STRUCTURE OF PIF1 HELICASE FROM BACTEROIDES IN COMPLEX WITH AMPPNP
 
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 :  1.38
Chains :  Asym./Biol. Unit :  A
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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2K9Ligand/IonPOTASSIUM ION
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:134 , HOH A:2052 , HOH A:2053 , HOH A:2054 , HOH A:2287 , HOH A:2288 , HOH A:2295BINDING SITE FOR RESIDUE K A1432
02AC2SOFTWAREMET A:4 , ILE A:5 , MET A:10 , ALA A:30 , GLY A:31 , SER A:32 , GLY A:33 , LYS A:34 , THR A:35 , THR A:36 , GLN A:145 , PHE A:187 , ARG A:188 , GLY A:365 , ARG A:390 , MG A:1435 , HOH A:2085 , HOH A:2090 , HOH A:2308 , HOH A:2376 , HOH A:2716 , HOH A:2717 , HOH A:2718BINDING SITE FOR RESIDUE ANP A1434
03AC3SOFTWARETHR A:35 , ANP A:1434 , HOH A:2090 , HOH A:2091 , HOH A:2092 , HOH A:2716BINDING SITE FOR RESIDUE MG A1435
04AC4SOFTWARETHR A:7 , GLU A:8 , GLU A:9 , HOH A:2008BINDING SITE FOR RESIDUE K A1436
05AC5SOFTWARECYS A:234 , THR A:235 , HIS A:236 , ASP A:239 , HOH A:2448 , HOH A:2452BINDING SITE FOR RESIDUE K A1437
06AC6SOFTWAREHIS A:274 , HOH A:2039 , HOH A:2522BINDING SITE FOR RESIDUE K A1438
07AC7SOFTWAREASN A:199 , ASN A:200 , ASN A:203 , GLN A:205 , HOH A:2398 , HOH A:2399BINDING SITE FOR RESIDUE K A1439
08AC8SOFTWAREPHE A:168 , ASN A:169 , ALA A:170 , LYS A:174 , TYR A:428 , HOH A:2354BINDING SITE FOR RESIDUE K A1440
09AC9SOFTWAREASP A:307 , ARG A:324BINDING SITE FOR RESIDUE K A1441
10BC1SOFTWAREPHE A:25 , THR A:27 , ASP A:142 , LEU A:143 , HOH A:2321BINDING SITE FOR RESIDUE K A1442

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FTB)

(-) 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:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh....eeeee.hhhhhhhhh.eehhhhhh................hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhheeeee..........hhhhhhhhh......hhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhh......hhhhhhh..hhhhhh......eeee.hhhhhhhhhhhhhh....eeee.eeee..hhhhh....eeee....eeee.............eeeeeee....eeeee....eeee..eeeeeeeeeee..eeeeeeeeeeee..eee..eeehhhhh......eee........hhhhhhhhh..hhh.eee....hhhhh..hhhhhhhhhhhhhh..eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ftb 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
   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 5FTB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

5ftc CRYSTAL STRUCTURE OF PIF1 HELICASE FROM BACTEROIDES IN COMPLEX WITH ADP
5ftd CRYSTAL STRUCTURE OF PIF1 HELICASE FROM BACTEROIDES APO FORM
5fte CRYSTAL STRUCTURE OF PIF1 HELICASE FROM BACTEROIDES IN COMPLEX WITH ADP-ALF3 AND SSDNA
5ftf CRYSTAL STRUCTURE OF PIF1 HELICASE FROM BACTEROIDES DOUBLE MUTANT L95C-I339C