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(-) Description

Title :  MOBM RELAXASE DOMAIN (MOBV; MOB_PRE) BOUND TO PLASMID PMV158 ORIT DNA (23NT). MN-BOUND CRYSTAL STRUCTURE AT PH 6.5
 
Authors :  R. Pluta, D. R. Boer, M. Coll
Date :  26 Jul 13  (Deposition) - 24 Sep 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Protein-Dna Complex, Pfam Family: Mob_pre (Pf01076). Mob Relaxase Family: Mobv, Relaxase/Endonuclease, Orit Dna, Dna Binding Protein- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Pluta, D. R. Boer, S. Russi, C. Fernandez-Lopez, F. Lorenzo-Diaz, R. Perez-Luque, M. Espinosa, M. Coll
Structures Of Dna-Mobm Relaxase Complexes Reveal A Histidine/Metal Catalysis For Dna Cleavage And Ligation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PLASMID RECOMBINATION ENZYME
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-1
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PALSMID
    Fragment: RELAXASE DOMAIN OF MOBM PROTEIN, UNP RESIDUES 2-199
    Gene: PRE, MOB
    Organism Scientific: STREPTOCOCCUS AGALACTIAE
    Organism Taxid: 1311
    Synonym: MOBILIZATION PROTEIN
 
Molecule 2 - ACTTTAT OLIGONUCLEOTIDE
    Chains: B, D
    Engineered: YES
    Fragment: OLIGONUCLEOTIDE_1 MIMICKING PMV158 ORIT DNA HAIRPIN
    Other Details: OLIGONUCLEOTIDES WERE OBTAINED FROM BIOMERS (ULM, GERMANY).
    Synthetic: YES
 
Molecule 3 - ATAAAGTATAGTGTGT OLIGONUCLEOTIDE
    Chains: E, F
    Engineered: YES
    Fragment: OLIGONUCLEOTIDE_2 MIMICKING PMV158 ORIT DNA HAIRPIN
    Other Details: OLIGONUCLEOTIDES WERE OBTAINED FROM BIOMERS (ULM, GERMANY).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION
3MN2Ligand/IonMANGANESE (II) ION
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MN-1Ligand/IonMANGANESE (II) ION
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MN-1Ligand/IonMANGANESE (II) ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:22 , HIS A:126 , GLU A:129 , HIS A:133 , HIS A:135 , DG E:26BINDING SITE FOR RESIDUE MN A 201
2AC2SOFTWAREMET A:199 , DA F:21BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWAREASP A:34 , GLU A:113 , ASP A:128 , GLU A:129BINDING SITE FOR RESIDUE CL A 203
4AC4SOFTWAREASN A:181BINDING SITE FOR RESIDUE NA A 204
5AC5SOFTWAREHIS C:22 , HIS C:126 , GLU C:129 , HIS C:133 , HIS C:135 , HOH C:308BINDING SITE FOR RESIDUE MN C 201
6AC6SOFTWAREGLN C:58BINDING SITE FOR RESIDUE CL C 202
7AC7SOFTWAREDA B:1 , ASN C:36 , SER C:38 , ARG C:39BINDING SITE FOR RESIDUE CL C 203
8AC8SOFTWAREASN C:36 , GLU C:129 , SER C:130BINDING SITE FOR RESIDUE CL C 204
9AC9SOFTWAREHIS C:186 , DT F:23BINDING SITE FOR RESIDUE CL F 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LVM)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhh.......................hhhhhhhhhhhhhh............eeeeeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeee..ee..eehhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lvm A   2 SYMVARMQKMKAGNLGGAFKHNERVKDINPSRSHLNYELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKDFFEKLDEEQTRTFFETAKNYFAENYGESNIAYASVHLDESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPRYMSDHGFELERGKLNSEAKHKTVAEFKRAMADM 199
                                    11        21    ||  37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197  
                                                   26|                                                                                                                                                                      
                                                    33                                                                                                                                                                      


Chain B from PDB  Type:DNA  Length:7
                                       
                 4lvm B   1 ACTTTAT   7


Chain C from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhh...........hhhhhh..ee........hhhhhhhhhhhh..............eeeeeee.hhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeee..ee..eehhhhhhhhhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lvm C   2 SYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLNYELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKDFFEKLDEEQTRTFFETAKNYFAENYGESNIAYASVHLDESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPRYMSDHGFELERGKLNSEAKHKTVAEF 192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 


Chain D from PDB  Type:DNA  Length:7
                                       
                 4lvm D   1 ACTTTAT   7


Chain E from PDB  Type:DNA  Length:16
                                                
                 4lvm E  12 ATAAAGTATAGTGTGT  27
                                    21      


Chain F from PDB  Type:DNA  Length:14
                                              
                 4lvm F  12 ATAAAGTATAGTGT  25
                                    21
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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 4LVM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRE_STRAG | P13925: 4lvi 4lvj 4lvk 4lvl 5n2q

(-) Related Entries Specified in the PDB File

4lvi 4lvj 4lvk 4lvl