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(-) Description

Title :  RESTRICTION ENDONUCLEASE BCNI-COGNATE DNA SUBSTRATE COMPLEX
 
Authors :  M. Sokolowska, M. Kaus-Drobek, H. Czapinska, G. Tamulaitis, R. H. Szczepanowski, C. Urbanke, V. Siksnys, M. Bochtler
Date :  22 Dec 06  (Deposition) - 20 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Endonuclease-Dna Complex, Restriction Enzyme, Bcni, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sokolowska, M. Kaus-Drobek, H. Czapinska, G. Tamulaitis, R. H. Szczepanowski, C. Urbanke, V. Siksnys, M. Bochtler
Monomeric Restriction Endonuclease Bcni In The Apo Form And In An Asymmetric Complex With Target Dna.
J. Mol. Biol. V. 369 722 2007
PubMed-ID: 17445830  |  Reference-DOI: 10.1016/J.JMB.2007.03.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3'
    Chains: D, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - R.BCNI
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PBAD24
    Expression System Vector Type: PLASMID
    Gene: BCNIR
    Organism Scientific: BREVIBACILLUS CENTROSPORUS
    Organism Taxid: 54910

 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  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:55 , GLU A:60 , LEU A:61 , HOH A:707 , DC C:0 , HOH C:7BINDING SITE FOR RESIDUE CA A 701
2AC2SOFTWAREASN A:49 , ASP A:55 , HOH A:749 , HOH A:768 , DC C:-1 , DC C:0BINDING SITE FOR RESIDUE CA A 703
3AC3SOFTWARETHR A:85 , VAL A:86 , HOH A:861 , HOH C:43BINDING SITE FOR RESIDUE CL A 705
4AC4SOFTWAREASP B:55 , GLU B:60 , LEU B:61 , HOH B:736 , DC E:0 , HOH E:80BINDING SITE FOR RESIDUE CA B 702
5AC5SOFTWARETHR B:85 , VAL B:86 , HOH B:714 , HOH B:883BINDING SITE FOR RESIDUE CL B 704

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ODI)

(-) 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:238
 aligned with Q8RNV8_9BACL | Q8RNV8 from UniProtKB/TrEMBL  Length:238

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q8RNV8_9BACL     1 MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..ee..........hhhhhhhhhhh...............eeeeee.......eeeee....ee.hhhhhhhhhheeee.......eeeeeeeee.........eeeeeee..eeeeee..eeeeee...hhhhh.eeeeeeeee........eeeeeeeeeeeee..hhhhhhh...eeeeeeeee.......ee...eeeehhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2odi A   1 mKIWSKEEVVNKLHEIKNKGYLSVPTDmFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGmRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVmKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYmLTEINDITSLINDGVLVmDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
                            |       10        20       |30        40        50        60   |    70        80        90       100     | 110       120       130       140       150       160       170       180|      190       200       210       220       230        
                            |                         28-MSE                              64-MSE                                   106-MSE                                                                    181-MSE           199-MSE                                   
                            1-MSE                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with Q8RNV8_9BACL | Q8RNV8 from UniProtKB/TrEMBL  Length:238

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q8RNV8_9BACL     1 MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...ee.hhhhh....hhhhhhhhhhh...............eeeeee.......eeeee....ee.hhhhhhhhhheeee.......eeeeeeeee.........eeeeeee..eeeeee..eeeeee...hhhhh.eeeeeeeee........eeeeeeeeeeeee.hhhhhhhh...eeeeeeeee......eee...eeeehhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2odi B   1 mKIWSKEEVVNKLHEIKNKGYLSVPTDmFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGmRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVmKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYmLTEINDITSLINDGVLVmDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
                            |       10        20       |30        40        50        60   |    70        80        90       100     | 110       120       130       140       150       160       170       180|      190       200       210       220       230        
                            1-MSE                     28-MSE                              64-MSE                                   106-MSE                                                                    181-MSE           199-MSE                                   


Chain C from PDB  Type:DNA  Length:11
                                           
                 2odi C  -4 AACCCGGAGAC   6
                                     5 


Chain D from PDB  Type:DNA  Length:11
                                           
                 2odi D  -4 CTCCGGGTTGT   6
                                     5 


Chain E from PDB  Type:DNA  Length:11
                                           
                 2odi E  -4 AACCCGGAGAC   6
                                     5 


Chain F from PDB  Type:DNA  Length:11
                                           
                 2odi F  -4 CTCCGGGTTGT   6
                                     5
   Legend:   → Mismatch (orange background)
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    → 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 2ODI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8RNV8_9BACL | Q8RNV8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  2odi
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 Related Entries

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

UniProtKB/TrEMBL
        Q8RNV8_9BACL | Q8RNV8: 2odh 2q10 3imb

(-) Related Entries Specified in the PDB File

2odh RESTRICTION ENDONUCLEASE BCNI IN THE ABSENCE OF DNA