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(-) Description

Title :  CRYSTAL STRUCTURE OF R.NGOAVII RESTRICTION ENDONUCLEASE B3 DOMAIN WITH COGNATE DNA
 
Authors :  G. Tamulaitiene, A. Silanskas, S. Grazulis, M. Zaremba, V. Siksnys
Date :  19 Sep 14  (Deposition) - 24 Dec 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
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, B3 Domain, Protein-Dna Complex, Hydrolase- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Tamulaitiene, A. Silanskas, S. Grazulis, M. Zaremba, V. Siksnys
Crystal Structure Of The R-Protein Of The Multisubunit Atp-Dependent Restriction Endonuclease Ngoavii.
Nucleic Acids Res. V. 42 14022 2014
PubMed-ID: 25429979  |  Reference-DOI: 10.1093/NAR/GKU1237

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE R.NGOVII
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLATE31
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NGK_0521, NGO0364
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 242231
    Strain: ATCC 700825 / FA 1090
 
Molecule 2 - DNA (5'-D(*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3) '
    Chains: C, E
    Engineered: YES
    Other Details: SYNTHETIC CONSTRUCT
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*G)-3) '
    Chains: D, F
    Engineered: YES
    Other Details: SYNTHETIC CONSTRUCT
    Synthetic: YES

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:300 , HIS A:304 , LYS A:342BINDING SITE FOR RESIDUE SO4 A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RDM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RDM)

(-) 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:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.hhhhhhhhh......eeeee......hhhhhhhh..ee.....ee........ee.hhhhhh........eeeeee...eeeeeeeehhhh.eeee...hhhhhhhhhhhhhhh.........hhhhhhhhh..eeeee......eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rdm A 180 HLENCLGVQKIAPEQIRQLFAQTSEYHFSIPAKTEEKSNLNVFFGEGRRDKRGFVKPRPWYEVELIVSKDITSQEGYPVLKSFTVITDDGWQFQCKTSGDYSKNFRSENDLKTLGKWIKGRLESHGCLQNNEKITHETLREYGNDHFELRSTDNPDVWLLSFKGK 344
                                   189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     


Chain B from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.hhhhhhhhhhh....eeeee......hhhhhhhh..ee.....ee........ee.hhhhhh........eeeeee...eeeeeeeehhhh.eeee...hhhhhhhhhhhhhhh.........hhhhhhhhh..eeeeee.....eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rdm B 181 LENCLGVQKIAPEQIRQLFAQTSEYHFSIPAKTEEKSNLNVFFGEGRRDKRGFVKPRPWYEVELIVSKDITSQEGYPVLKSFTVITDDGWQFQCKTSGDYSKNFRSENDLKTLGKWIKGRLESHGCLQNNEKITHETLREYGNDHFELRSTDNPDVWLLSFKGK 344
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    


Chain C from PDB  Type:DNA  Length:15
                                               
                 4rdm C   2 CCTAAGCGGCAATCC  16
                                    11     


Chain D from PDB  Type:DNA  Length:15
                                               
                 4rdm D  17 GGGATTGCCGCCTAG  31
                                    26     


Chain E from PDB  Type:DNA  Length:14
                                              
                 4rdm E   3 CTAAGCGGCAATCC  16
                                    12    


Chain F from PDB  Type:DNA  Length:15
                                               
                 4rdm F  17 GGGATTGCCGCCTAG  31
                                    26
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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 4RDM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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        Q5F9M9_NEIG1 | Q5F9M9: 4rct 4rd5

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