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(-) Description

Title :  TIME-RESOLVED CRYSTAL STRUCTURE OF HINDIII WITH 60SEC SOAKING
 
Authors :  T. Kawamura, T. Kobayashi, N. Watanabe
Date :  02 Jun 14  (Deposition) - 08 Apr 15  (Release) - 08 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Biol. Unit 1:  A,B,G,H  (1x)
Biol. Unit 2:  A,B,M,N,O,P  (1x)
Biol. Unit 3:  C,D,E,F  (1x)
Biol. Unit 4:  C,D,Q,R,S,T  (1x)
Biol. Unit 5:  I,J  (1x)
Biol. Unit 6:  K,L  (1x)
Keywords :  Freeze-Trap, Time-Resolved, Type Ii Restriction Enzyme, Hydrolase, Endonuclease, 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: C, D, A, B
    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: K, L, I, J, E, F, G, H
    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
 
Molecule 3 - DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3')
    Chains: M, N, Q, R
    Engineered: YES
    Fragment: 3'-FRAGMENT OF CLEAVED COGNATE DNA
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*GP*CP*CP*A)-3')
    Chains: O, P, S, T
    Engineered: YES
    Fragment: 5'-FRAGMENT OF CLEAVED COGNATE DNA
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567891011121314151617181920
Asymmetric Unit : ABCDEFGHIJKLMNOPQRST
Biological Unit 1 (1x): AB    GH            
Biological Unit 2 (1x): AB          MNOP    
Biological Unit 3 (1x):   CDEF              
Biological Unit 4 (1x):   CD            QRST
Biological Unit 5 (1x):         IJ          
Biological Unit 6 (1x):           KL        

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 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE 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
02AC2SOFTWAREASP C:93 , ASP C:108 , ALA C:109 , HOH C:466 , DA F:5 , HOH F:106 , DA R:1BINDING SITE FOR RESIDUE MN C 302
03AC3SOFTWAREGLN C:87 , ASP C:93 , HOH C:467 , HOH C:468 , HOH C:470 , DA F:4 , DA F:5 , DA R:1 , DA S:4BINDING SITE FOR RESIDUE MN C 303
04AC4SOFTWAREARG C:296 , TYR C:298 , PHE D:145 , PHE D:146 , TYR D:148 , PRO D:149 , ASN D:210 , MET D:212BINDING SITE FOR RESIDUE GOL D 301
05AC5SOFTWAREASP D:93 , ASP D:108 , ALA D:109 , HOH D:471 , HOH D:474 , DA E:5 , DA Q:1BINDING SITE FOR RESIDUE MN D 302
06AC6SOFTWAREGLN D:87 , ASP D:93 , HOH D:472 , HOH D:477 , DA E:4 , DA E:5 , DA Q:1 , DA T:4 , HOH T:104BINDING SITE FOR RESIDUE MN D 303
07AC7SOFTWAREPHE 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 A 301
08AC8SOFTWAREARG A:296 , TYR A:298 , PHE B:145 , PHE B:146 , TYR B:148 , ASN B:210 , MET B:212BINDING SITE FOR RESIDUE GOL A 302
09AC9SOFTWAREASP A:93 , ASP A:108 , ALA A:109 , HOH A:452 , DA H:5 , HOH H:107 , DA M:1BINDING SITE FOR RESIDUE MN A 303
10BC1SOFTWAREGLN A:87 , ASP A:93 , HOH A:453 , HOH A:454 , HOH A:457 , DA H:4 , DA H:5 , DA M:1 , DA P:4BINDING SITE FOR RESIDUE MN A 304
11BC2SOFTWAREASP B:93 , ASP B:108 , ALA B:109 , HOH B:466 , DA G:5 , HOH G:104 , DA N:1BINDING SITE FOR RESIDUE MN B 301
12BC3SOFTWAREGLN B:87 , ASP B:93 , HOH B:467 , HOH B:469 , DA G:4 , DA G:5 , DA N:1 , DA O:4 , HOH O:104BINDING SITE FOR RESIDUE MN B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WVP)

(-) 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.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh..eeeee.........eeeee.....eeeeee..........hhhhhhhhhhhhhh....eeeeeehhhhh....hhhhhhhhhhh.eeeehhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wvp 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..eeee.........eeee......eeeeee..ee......hhhhhhhhhhhhhh....eeeeeehhhhh....hhhhhhhhhhh.eeeehhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wvp 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.eeeee.........eeeee.....eeeeee..ee......hhhhhhhhhhhhhh....eeeeeehhhhh....hhhhhhhhhhh.eeeehhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wvp 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.hhhhhhhhhh...ee.......hhhhhhhhhhhhhhhhhhhhhh.eeeee.........eeeee.....eeeeee..ee......hhhhhhhhhhhhhh....eeeeeehhhhh....hhhhhhhhhhh.eeeehhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wvp 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
                                            
                 3wvp E   1 GCCAAGCTTGGC  12
                                    10  


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


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


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


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


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


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


Chain L from PDB  Type:DNA  Length:12
                                            
                 3wvp L   1 GCCAAGCTTGGC  12
                                    10  


Chain M from PDB  Type:DNA  Length:8
                                        
                 3wvp M   1 AGCTTGGC   8


Chain N from PDB  Type:DNA  Length:8
                                        
                 3wvp N   1 AGCTTGGC   8


Chain O from PDB  Type:DNA  Length:4
                                    
                 3wvp O   1 GCCA   4


Chain P from PDB  Type:DNA  Length:4
                                    
                 3wvp P   1 GCCA   4


Chain Q from PDB  Type:DNA  Length:8
                                        
                 3wvp Q   1 AGCTTGGC   8


Chain R from PDB  Type:DNA  Length:8
                                        
                 3wvp R   1 AGCTTGGC   8


Chain S from PDB  Type:DNA  Length:4
                                    
                 3wvp S   1 GCCA   4


Chain T from PDB  Type:DNA  Length:4
                                    
                 3wvp T   1 GCCA   4
   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 3WVP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  3wvp
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  T2D3_HAEIN | P43870
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 Related Entries

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

UniProtKB/Swiss-Prot
        T2D3_HAEIN | P43870: 2e52 3a4k 3wvg 3wvh 3wvi 3wvk

(-) Related Entries Specified in the PDB File

3wvg 3wvh 3wvi 3wvk