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(-) Description

Title :  TIME-RESOLVED CRYSTAL STRUCTURE OF HINDIII WITH 40 SEC SOAKING
 
Authors :  T. Kawamura, T. Kobayashi, N. Watanabe
Date :  21 May 14  (Deposition) - 08 Apr 15  (Release) - 08 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Biol. Unit 3:  K,L  (1x)
Biol. Unit 4:  I,J  (1x)
Keywords :  Freeze-Trap, Type Iip Restriction Endonuclease, Endonuclease, Hydrolase, Nuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kawamura, T. Kobayashi, N. Watanabe
Analysis Of The Hindiii-Catalyzed Reaction By Time-Resolved Crystallography
Acta Crystallogr. , Sect. D V. 71 256 2015
PubMed-ID: 25664735  |  Reference-DOI: 10.1107/S1399004714025188

(-) Compounds

Molecule 1 - TYPE-2 RESTRICTION ENZYME HINDIII
    Chains: A, B, C, D
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HINDIIIR, HI_1393
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 71421
    Strain: RD KW20
    Synonym: R.HINDIII, ENDONUCLEASE HINDIII, TYPE II RESTRICTION ENZYME HINDIII
 
Molecule 2 - DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
    Chains: F, E, H, G, K, L, I, J
    Engineered: YES
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Other Details: THIS DNA SEQUENCE SYNTHESIZED CHEMICALLY CONTAINS COGNATE HINDIIIR RECOGNITION SEQUENCE AND ELONGATED SCAFFOLDS ON BOTH SIDES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): AB  EF      
Biological Unit 2 (1x):   CD  GH    
Biological Unit 3 (1x):           KL
Biological Unit 4 (1x):         IJ  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MN8Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:93 , ASP A:108 , ALA A:109 , HOH A:478 , HOH A:486 , DA E:5BINDING SITE FOR RESIDUE MN A 301
02AC2SOFTWAREPHE A:145 , PHE A:146 , TYR A:148 , PRO A:149 , ASN A:210 , MET A:212 , ARG B:296 , TYR B:298BINDING SITE FOR RESIDUE GOL B 301
03AC3SOFTWAREARG A:296 , TYR A:298 , PHE B:145 , PHE B:146 , TYR B:148 , THR B:150 , ASN B:210 , MET B:212BINDING SITE FOR RESIDUE GOL B 302
04AC4SOFTWAREASP B:93 , ASP B:108 , ALA B:109 , HOH B:471 , HOH B:483 , DA F:5BINDING SITE FOR RESIDUE MN B 303
05AC5SOFTWAREPHE C:145 , PHE C:146 , TYR C:148 , PRO C:149 , ASN C:210 , MET C:212 , ARG D:296 , TYR D:298BINDING SITE FOR RESIDUE GOL C 301
06AC6SOFTWAREARG C:296 , TYR C:298 , PHE D:145 , PHE D:146 , TYR D:148 , ASN D:210 , MET D:212BINDING SITE FOR RESIDUE GOL C 302
07AC7SOFTWAREASP C:93 , ASP C:108 , ALA C:109 , HOH C:459 , HOH C:465 , DA G:5BINDING SITE FOR RESIDUE MN C 303
08AC8SOFTWAREASP D:93 , ASP D:108 , ALA D:109 , HOH D:471 , DA H:5 , HOH H:115BINDING SITE FOR RESIDUE MN D 301
09AC9SOFTWAREASP D:93 , HOH D:469 , HOH D:470 , HOH D:472 , DA H:4 , DA H:5BINDING SITE FOR RESIDUE MN D 302
10BC1SOFTWAREASP B:93 , HOH B:472 , HOH B:473 , HOH B:474 , DA F:4 , DA F:5BINDING SITE FOR RESIDUE MN F 101
11BC2SOFTWAREASP A:93 , HOH A:479 , HOH A:480 , HOH A:481 , DA E:4 , DA E:5BINDING SITE FOR RESIDUE MN E 101
12BC3SOFTWAREASP C:93 , HOH C:460 , HOH C:461 , HOH C:462 , DA G:4 , DA G:5BINDING SITE FOR RESIDUE MN G 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WVI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WVI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WVI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WVI)

(-) Exons   (0, 0)

(no "Exon" information available for 3WVI)

(-) 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:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhh.ee.......hhhhhhhhhhhhhhhhhhhhhh.eeeee.........eeeee.....eeeeee..ee......hhhhhhhhhhhhhh....eeeeeehhhhh....hhhhhhhhhhheeeeehhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wvi A   2 KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        


Chain B from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhh.ee.......hhhhhhhhhhhhhhhhhhhhhh.eeeee.........eeeee.....eeeeee..ee......hhhhhhhhhhhhhh....eeeeeehhhhh....hhhhhhhhhhheeeeehhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wvi B   2 KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        


Chain C from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhh.ee.......hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee......eeeeee..ee......hhhhhhhhhhhhh.....eeeeeehhhhh....hhhhhhhhhhheeeeehhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wvi C   2 KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        


Chain D from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhee.......hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee......eeeeee..ee......hhhhhhhhhhhhhh....eeeeeehhhhh....hhhhhhhhhhh.eeeehhhhhhhhhh.........hhhhhhhhhhhhh..........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wvi D   2 KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPEAIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEFNYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTKSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKTSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYWKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        


Chain E from PDB  Type:DNA  Length:12
                                            
                 3wvi E   1 GCCAAGCTTGGC  12
                                    10  


Chain F from PDB  Type:DNA  Length:12
                                            
                 3wvi F   1 GCCAAGCTTGGC  12
                                    10  


Chain G from PDB  Type:DNA  Length:12
                                            
                 3wvi G   1 GCCAAGCTTGGC  12
                                    10  


Chain H from PDB  Type:DNA  Length:12
                                            
                 3wvi H   1 GCCAAGCTTGGC  12
                                    10  


Chain I from PDB  Type:DNA  Length:12
                                            
                 3wvi I   1 GCCAAGCTTGGC  12
                                    10  


Chain J from PDB  Type:DNA  Length:12
                                            
                 3wvi J   1 GCCAAGCTTGGC  12
                                    10  


Chain K from PDB  Type:DNA  Length:12
                                            
                 3wvi K   1 GCCAAGCTTGGC  12
                                    10  


Chain L from PDB  Type:DNA  Length:12
                                            
                 3wvi L   1 GCCAAGCTTGGC  12
                                    10
   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 3WVI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WVI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WVI)

(-) Gene Ontology  (6, 6)

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  3wvi
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  T2D3_HAEIN | P43870
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  3.1.21.4
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        T2D3_HAEIN | P43870: 2e52 3a4k 3wvg 3wvh 3wvk 3wvp

(-) Related Entries Specified in the PDB File

3wvg 3wvh 3wvk 3wvp