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(-) Description

Title :  RESTRICTION/MODIFICATION SYSTEM-TYPE II R.SWAI CLEAVED DNA COMPLEX
 
Authors :  B. W. Shen, B. L. Stoddard
Date :  29 Sep 16  (Deposition) - 21 Dec 16  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,B,C,D,H,I,J,K,h,i,j,k
Biol. Unit 1:  A,B,H,I,h,i  (1x)
Biol. Unit 2:  C,D,J,K,j,k  (1x)
Keywords :  I-Swai, Cleaved Dna Complex, R/M System, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. W. Shen, D. F. Heiter, K. D. Lunnen, G. G. Wilson, B. L. Stoddard
Dna Recognition By The Swai Restriction Endonuclease Involves Unusual Distortion Of An 8 Base Pair A:T-Rich Target.
Nucleic Acids Res. V. 45 1516 2017
PubMed-ID: 28180307  |  Reference-DOI: 10.1093/NAR/GKW1200

(-) Compounds

Molecule 1 - R-SWAI PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: ER2566
    Expression System Plasmid: PHKT7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: STAPHYLOCOCCUS WARNERI
    Organism Taxid: 1292
 
Molecule 2 - DNA (CLEAVED 25-MER, PORTION 1)
    Chains: H, J
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (CLEAVED 25-MER, PORTION 2)
    Chains: h, j
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (CLEAVED 26-MER, PORTION 1)
    Chains: I, K
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 5 - DNA (CLEAVED 26-MER, PORTION 2)
    Chains: i, k
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDHIJKhijk
Biological Unit 1 (1x): AB  HI  hi  
Biological Unit 2 (1x):   CD  JK  jk

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 30)

Asymmetric Unit (4, 30)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MG6Ligand/IonMAGNESIUM ION
4MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
4MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
4MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:76 , ASP A:93 , PHE A:94 , MG A:302 , HOH A:414 , HOH A:424 , DA h:25binding site for residue MG A 301
02AC2SOFTWAREASP A:76 , ASP A:93 , MG A:301 , HOH A:424 , DT H:14 , DA h:25 , HOH h:104binding site for residue MG A 302
03AC3SOFTWAREGLY A:65 , ALA A:66 , PRO A:67 , TYR D:61 , ASP D:62binding site for residue EDO A 303
04AC4SOFTWAREASP B:76 , ASP B:93 , PHE B:94 , HOH B:406 , HOH B:417 , DA i:25 , HOH i:202binding site for residue MG B 301
05AC5SOFTWAREPHE B:141 , TYR B:148binding site for residue ACT B 302
06AC6SOFTWAREASP C:76 , ASP C:93 , PHE C:94 , HOH C:410 , HOH C:413 , DA j:25 , HOH j:102binding site for residue MG C 301
07AC7SOFTWAREASP D:76 , ASP D:93 , PHE D:94 , MG D:302 , HOH D:409 , HOH D:420 , DA k:25binding site for residue MG D 301
08AC8SOFTWAREASP D:76 , ASP D:93 , MG D:301 , HOH D:420 , DT K:14 , DA k:25binding site for residue MG D 302
09AC9SOFTWAREPHE D:3 , GLU D:7 , LYS D:155 , TYR D:179 , THR D:181 , ARG D:182binding site for residue EDO D 303
10AD1SOFTWAREDC I:7 , DG I:8 , DG I:9 , DG h:29binding site for residue EDO I 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TH3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:166 -Pro A:167
2Lys B:166 -Pro B:167
3Lys C:166 -Pro C:167
4Lys D:166 -Pro D:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TH3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TH3)

(-) Exons   (0, 0)

(no "Exon" information available for 5TH3)

(-) 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeeee...........eeeeeee..eeeeeeeeeeeee........eeehhhhhhhhhhh...eeeeeeeeeeee..eeee.......eeeee.hhh....eee...eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5th3 A   1 mNFKKYEENLVASIEEVIQRIIDDKHRPNIIGKTRVGAEVSDYLEDEFVKYISSGKSSSLYDAQGAPKEKTKNPWDARCKFKFmDREEEIWIDFKAFKITNmDSNPDIGTPNKIVKFIHEGNFYLVFVLVYYESKQDGVEFVKYNNDYKKVYLLKDVNESFRINPKPQmQVNIAAEPTYRTREEFIHFFVKKWKESFERQIKSLEKKEImLKDLEDKLKNSNDNSI 226
                            |       10        20        30        40        50        60        70        80   |    90       100 |     110       120       130       140       150       160       170       180       190       200       210       220      
                            |                                                                                 84-MSE           102-MSE                                                            169-MSE                                  210-MSE            
                            1-MSE                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeeee...........eeeeeee..eeeeeeeeeeeee........eeehhhhhhhhhhh...eeeeeeeeeeee..eeee.......eeeee.hhh....eee...eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5th3 B   1 mNFKKYEENLVASIEEVIQRIIDDKHRPNIIGKTRVGAEVSDYLEDEFVKYISSGKSSSLYDAQGAPKEKTKNPWDARCKFKFmDREEEIWIDFKAFKITNmDSNPDIGTPNKIVKFIHEGNFYLVFVLVYYESKQDGVEFVKYNNDYKKVYLLKDVNESFRINPKPQmQVNIAAEPTYRTREEFIHFFVKKWKESFERQIKSLEKKEImLKDLEDKLKNSNDNSI 226
                            |       10        20        30        40        50        60        70        80   |    90       100 |     110       120       130       140       150       160       170       180       190       200       210       220      
                            1-MSE                                                                             84-MSE           102-MSE                                                            169-MSE                                  210-MSE            


Chain C from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeeee...........eeeeeee..eeeeeeeeeeeee...........hhhhhhhhhhh...eeeeeeeeeeee..eeee.......eeeee.hhh....eee...eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5th3 C   1 mNFKKYEENLVASIEEVIQRIIDDKHRPNIIGKTRVGAEVSDYLEDEFVKYISSGKSSSLYDAQGAPKEKTKNPWDARCKFKFmDREEEIWIDFKAFKITNmDSNPDIGTPNKIVKFIHEGNFYLVFVLVYYESKQDGVEFVKYNNDYKKVYLLKDVNESFRINPKPQmQVNIAAEPTYRTREEFIHFFVKKWKESFERQIKSLEKKEImLKDLEDKLKNSNDNSI 226
                            |       10        20        30        40        50        60        70        80   |    90       100 |     110       120       130       140       150       160       170       180       190       200       210       220      
                            1-MSE                                                                             84-MSE           102-MSE                                                            169-MSE                                  210-MSE            


Chain D from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeeee...........eeeeeee..eeeeeeeeeeeee........eeehhhhhhhhhhh...eeeeeeeeeeee..eeee.......eeeee.hhh....eee...eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5th3 D   1 mNFKKYEENLVASIEEVIQRIIDDKHRPNIIGKTRVGAEVSDYLEDEFVKYISSGKSSSLYDAQGAPKEKTKNPWDARCKFKFmDREEEIWIDFKAFKITNmDSNPDIGTPNKIVKFIHEGNFYLVFVLVYYESKQDGVEFVKYNNDYKKVYLLKDVNESFRINPKPQmQVNIAAEPTYRTREEFIHFFVKKWKESFERQIKSLEKKEImLKDLEDKLKNSNDNSI 226
                            |       10        20        30        40        50        60        70        80   |    90       100 |     110       120       130       140       150       160       170       180       190       200       210       220      
                            1-MSE                                                                             84-MSE           102-MSE                                                            169-MSE                                  210-MSE            


Chain H from PDB  Type:DNA  Length:12
                                            
                 5th3 H   3 GCGGAGGCATTT  14
                                    12  


Chain I from PDB  Type:DNA  Length:14
                                              
                 5th3 I   1 CCCGCGCGGCATTT  14
                                    10    


Chain J from PDB  Type:DNA  Length:14
                                              
                 5th3 J   1 GGGCGGAGGCATTT  14
                                    10    


Chain K from PDB  Type:DNA  Length:13
                                             
                 5th3 K   2 CCGCGCGGCATTT  14
                                    11   


Chain h from PDB  Type:DNA  Length:13
                                             
                 5th3 h  25 AAATGCCGCGCGG  37
                                    34   


Chain i from PDB  Type:DNA  Length:12
                                            
                 5th3 i  25 AAATGCCTCCGC  36
                                    34  


Chain j from PDB  Type:DNA  Length:13
                                             
                 5th3 j  25 AAATGCCGCGCGG  37
                                    34   


Chain k from PDB  Type:DNA  Length:13
                                             
                 5th3 k  25 AAATGCCTCCGCC  37
                                    34
   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 5TH3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TH3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TH3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5TH3)

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  5th3
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  A0A1S4NYF7_S | A0A1S4NYF7
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 Related Entries

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        A0A1S4NYF7_S | A0A1S4NYF7: 5tgq 5tgx

(-) Related Entries Specified in the PDB File

5tgq 5tgx