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(-) Description

Title :  CONJUGATIVE RELAXASE TRWC IN COMPLEX WITH ORIT DNA. METAL-FREE STRUCTURE.
 
Authors :  A. Guasch, M. Lucas, G. Moncalian, M. Cabezas, R. Perez-Luque, F. X. Gomis-Ruth, F. De La Cruz, M. Coll
Date :  19 Mar 03  (Deposition) - 25 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Bacterial Conjugation, Relaxase, Dna Replication, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Guasch, M. Lucas, G. Moncalian, M. Cabezas, R. Perez-Luque, F. X. Gomis-Ruth, F. De La Cruz, M. Coll
Recognition And Processing Of The Origin Of Transfer Dna By Conjugative Relaxase Trwc.
Nat. Struct. Biol. V. 10 1002 2003
PubMed-ID: 14625590  |  Reference-DOI: 10.1038/NSB1017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA OLIGONUCLEOTIDE
    Chains: B, D
    Engineered: YES
    Other Details: DNA FORMING A CRUCIFORM ARM
    Synthetic: YES
 
Molecule 2 - TRWC PROTEIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL RELAXASE DOMAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:3 , THR A:87 , LYS A:262 , HOH A:501 , HOH A:502 , DG B:22 , DC B:24 , DT B:25BINDING SITE FOR RESIDUE SO4 B 801
2AC2SOFTWAREHIS A:150 , HIS A:161 , HIS A:163 , SO4 A:803 , DT B:25BINDING SITE FOR RESIDUE SO4 B 802
3AC3SOFTWAREASP A:21 , HIS A:150 , GLU A:151 , THR A:152 , ARG A:274 , SO4 B:802BINDING SITE FOR RESIDUE SO4 A 803
4AC4SOFTWAREARG A:154BINDING SITE FOR RESIDUE SO4 A 804
5AC5SOFTWAREGLN A:176 , ARG A:278 , LYS C:53BINDING SITE FOR RESIDUE SO4 A 805
6AC6SOFTWAREARG C:14 , ARG C:154BINDING SITE FOR RESIDUE SO4 C 806
7AC7SOFTWARESER C:3 , THR C:87 , LYS C:262 , HOH C:657 , DG D:22 , DC D:24 , DT D:25 , HOH D:656 , HOH D:658BINDING SITE FOR RESIDUE SO4 D 807
8AC8SOFTWARELYS A:53 , HIS C:67 , ARG C:68BINDING SITE FOR RESIDUE SO4 C 808
9AC9SOFTWAREHIS C:150 , GLU C:151 , THR C:152 , ARG C:274BINDING SITE FOR RESIDUE SO4 C 809

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OSB)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:19 -Glu A:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OSB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OSB)

(-) Exons   (0, 0)

(no "Exon" information available for 1OSB)

(-) 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:287
 aligned with Q47673_ECOLX | Q47673 from UniProtKB/TrEMBL  Length:966

    Alignment length:293
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   
         Q47673_ECOLX     1 MLSHMVLTRQDIGRAASYYEDGADDYYAKDGDASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRIMRSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETTGNLVIGKFRHETSRERDPQLHTHAVILNMTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQLRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAEWQATAKELGIDFS 293
               SCOP domains d1osba_ A: TrwC relaxase                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhh.......------...eeeehhhhhhh......hhhhhhhhhh....................eeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.....eeeeeeee.....eeeeeeeeee..ee.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eee...hhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1osb A   1 MLSHMVLTRQDIGRAASYYEDGAD------GDASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRIMRSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETTGNLVIGKFRHETSRERDPQLHTHAVILNMTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQLRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAEWQATAKELGIDFS 293
                                    10        20   |     -|       40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   
                                                  24     31                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:DNA  Length:25
                                                         
                 1osb B   1 GCGCACCGAAAGGTGCGTATTGTCT  25
                                    10        20     


Chain C from PDB  Type:PROTEIN  Length:282
 aligned with Q47673_ECOLX | Q47673 from UniProtKB/TrEMBL  Length:966

    Alignment length:292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  
         Q47673_ECOLX     1 MLSHMVLTRQDIGRAASYYEDGADDYYAKDGDASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRIMRSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETTGNLVIGKFRHETSRERDPQLHTHAVILNMTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQLRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAEWQATAKELGIDF 292
               SCOP domains d1osbc_ C: TrwC rela          xase                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------TrwC-1osbC01           C:8-292                                                                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) -------TrwC-1osbC02           C:8-292                                                                                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author .eeeeeee..hhhhhhh...----------...eeeehhhhhhh......hhhhhhhhhh....................eeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.....eeeeeeee.....eeeeeeeeee..ee.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eee...hhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1osb C   1 MLSHMVLTRQDIGRAASYYE----------GDASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRIMRSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETTGNLVIGKFRHETSRERDPQLHTHAVILNMTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQLRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAEWQATAKELGIDF 292
                                    10        20         -|       40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  
                                              20         31                                                                                                                                                                                                                                                                     


Chain D from PDB  Type:DNA  Length:25
                                                         
                 1osb D   1 GCGCACCGAAAGGTGCGTATTGTCT  25
                                    10        20
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OSB)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: TrwC] (9)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q47673_ECOLX | Q47673)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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        Q47673_ECOLX | Q47673: 1omh 1qx0 1s6m 1zm5 2cdm 4pcb

(-) Related Entries Specified in the PDB File

1omh