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(-) Description

Title :  CRYSTAL FORM I OF PRE-REACTIVE COMPLEX OF RESTRICTION ENDONUCLEASE HINP1I WITH COGNATE DNA AND CALCIUM ION
 
Authors :  J. R. Horton
Date :  04 Jan 06  (Deposition) - 21 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Restriction Endonuclease, Protein Dimerizaton, Dna Superhelix, Protein-Dna-Metal Ion Complex, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Horton, X. Zhang, R. Maunus, Z. Yang, G. G. Wilson, R. J. Roberts, X. Cheng
Dna Nicking By Hinp1I Endonuclease: Bending, Base Flipping And Minor Groove Expansion.
Nucleic Acids Res. V. 34 939 2006
PubMed-ID: 16473850  |  Reference-DOI: 10.1093/NAR/GKJ484
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
    Chains: C, D, E, F
    Engineered: YES
    Other Details: SYNTHESIZED SELF-ANNEALING OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 2 - R.HINP1I RESTRICTION ENDONUCLEASE
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Strain: PR1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HINP1IR
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:62 , GLN A:81 , VAL A:82 , DC C:5 , HOH C:53BINDING SITE FOR RESIDUE CA A 248
2AC2SOFTWAREGLU A:18 , ASP A:62 , DG C:4 , DC C:5 , HOH C:54BINDING SITE FOR RESIDUE CA C 52
3AC3SOFTWAREASP B:62 , GLN B:81 , VAL B:82 , DC E:5 , HOH E:12BINDING SITE FOR RESIDUE CA B 248

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FKC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FKC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FKC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FKC)

(-) Exons   (0, 0)

(no "Exon" information available for 2FKC)

(-) 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:247
 aligned with Q5I6E6_HAEIF | Q5I6E6 from UniProtKB/TrEMBL  Length:247

    Alignment length:247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
         Q5I6E6_HAEIF     1 MNLVELGSKTAKDGFKNEKDIADRFENWKENSEAQDWLVTMGHNLDEIKSVKAVVLSGYKSDINVQVLVFYKDALDIHNIQVKLVSNKRGFNQIDKHWLAHYQEMWKFDDNLLRILRHFTGELPPYHSNTKDKRRMFMTEFSQEEQNIVLNWLEKNRVLVLTDILRGRGDFAAEWVLVAQKVSNNARWILRNINEVLQHYGSGDISLSPRGSINFGRVTIQRKGGDNGRETANMLQFKIDPTELFDI 247
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhh.eeeeeeee.......eeeeeee......eeeeeeeeee......eeeeeehhhhhhhhhh.hhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee....eeeeeeehhhhhhhhhh..eee.....eee..eeeee..hhhhhhhhh.eeeeehhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fkc A   1 MNLVELGSKTAKDGFKNEKDIADRFENWKENSEAQDWLVTMGHNLDEIKSVKAVVLSGYKSDINVQVLVFYKDALDIHNIQVKLVSNKRGFNQIDKHWLAHYQEMWKFDDNLLRILRHFTGELPPYHSNTKDKRRMFMTEFSQEEQNIVLNWLEKNRVLVLTDILRGRGDFAAEWVLVAQKVSNNARWILRNINEVLQHYGSGDISLSPRGSINFGRVTIQRKGGDNGRETANMLQFKIDPTELFDI 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with Q5I6E6_HAEIF | Q5I6E6 from UniProtKB/TrEMBL  Length:247

    Alignment length:247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
         Q5I6E6_HAEIF     1 MNLVELGSKTAKDGFKNEKDIADRFENWKENSEAQDWLVTMGHNLDEIKSVKAVVLSGYKSDINVQVLVFYKDALDIHNIQVKLVSNKRGFNQIDKHWLAHYQEMWKFDDNLLRILRHFTGELPPYHSNTKDKRRMFMTEFSQEEQNIVLNWLEKNRVLVLTDILRGRGDFAAEWVLVAQKVSNNARWILRNINEVLQHYGSGDISLSPRGSINFGRVTIQRKGGDNGRETANMLQFKIDPTELFDI 247
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhh.eeeeeeee.......eeeeeee......eeeeeeeeee......eeeeeehhhhhhhhhh.hhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeeehhhhhhhhh...eee.....eee..eeeee..hhhhhhhhh.eeeee..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fkc B   1 MNLVELGSKTAKDGFKNEKDIADRFENWKENSEAQDWLVTMGHNLDEIKSVKAVVLSGYKSDINVQVLVFYKDALDIHNIQVKLVSNKRGFNQIDKHWLAHYQEMWKFDDNLLRILRHFTGELPPYHSNTKDKRRMFMTEFSQEEQNIVLNWLEKNRVLVLTDILRGRGDFAAEWVLVAQKVSNNARWILRNINEVLQHYGSGDISLSPRGSINFGRVTIQRKGGDNGRETANMLQFKIDPTELFDI 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       


Chain C from PDB  Type:DNA  Length:10
                                          
                 2fkc C   1 CCAGCGCTGG  10
                                    10


Chain D from PDB  Type:DNA  Length:10
                                          
                 2fkc D  11 CCAGCGCTGG  20
                                    20


Chain E from PDB  Type:DNA  Length:10
                                          
                 2fkc E   1 CCAGCGCTGG  10
                                    10


Chain F from PDB  Type:DNA  Length:10
                                          
                 2fkc F  11 CCAGCGCTGG  20
                                    20
   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 2FKC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FKC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FKC)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5I6E6_HAEIF | Q5I6E6)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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  3.1.21.4
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5I6E6_HAEIF | Q5I6E6: 1ynm 2fkh 2fl3 2flc

(-) Related Entries Specified in the PDB File

1ynm THE SAME PROTEIN BUT NOT COMPLEXED WITH COGNATE DNA AND METAL ION.
2fkh
2fl3
2flc