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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BA-SOAKED C2 CRYSTAL FORM OF PMV158 REPLICATION INITIATOR REPB (P3221 SPACE GROUP)
 
Authors :  D. R. Boer, J. A. Ruiz Maso, G. Del Solar, M. Coll
Date :  01 Aug 14  (Deposition) - 26 Aug 15  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Dna Replication Initiator, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Boer, J. A. Ruiz-Maso, M. Rueda, M. V. Petoukhov, C. Machon, D. I. Svergun, M. Orozco, G. Del Solar, M. Coll
Conformational Plasticity Of Repb, The Replication Initiato Protein Of Promiscuous Streptococcal Plasmid Pmv158.
Sci Rep V. 6 20915 2016
PubMed-ID: 26875695  |  Reference-DOI: 10.1038/SREP20915

(-) Compounds

Molecule 1 - REPLICATION PROTEIN REPB
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEM-T
    Expression System Taxid: 469008
    Gene: REPB
    Organism Scientific: STREPTOCOCCUS AGALACTIAE
    Organism Taxid: 1311
    Synonym: REPLICATION INITATOR REPB

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1BA9Ligand/IonBARIUM ION
2CL3Ligand/IonCHLORIDE ION
3MN3Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BA-1Ligand/IonBARIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:185 , LYS B:186binding site for residue CL A 301
02AC2SOFTWAREHIS A:39 , ASP A:42 , HIS A:55 , HIS A:57 , HIS A:102binding site for residue MN A 302
03AC3SOFTWAREGLY B:185 , LYS C:186binding site for residue CL B 301
04AC4SOFTWAREASP B:129 , VAL B:132 , GLU B:181binding site for residue BA B 302
05AC5SOFTWAREASP B:166binding site for residue BA B 304
06AC6SOFTWAREGLU B:16 , LYS C:121binding site for residue BA B 305
07AC7SOFTWAREHIS B:39 , ASP B:42 , HIS B:55 , HIS B:57 , HIS B:102binding site for residue MN B 306
08AC8SOFTWARELYS A:186 , GLY C:185binding site for residue CL C 301
09AC9SOFTWAREASP C:129 , VAL C:132binding site for residue BA C 302
10AD1SOFTWARELYS B:63 , THR C:133 , GLU C:138binding site for residue BA C 303
11AD2SOFTWARESER C:44 , ILE C:46 , GLN C:49binding site for residue BA C 304
12AD3SOFTWAREASP C:166binding site for residue BA C 305
13AD4SOFTWAREGLU C:16binding site for residue BA C 306
14AD5SOFTWAREHIS C:39 , ASP C:42 , HIS C:55 , HIS C:57 , HIS C:102binding site for residue MN C 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U87)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U87)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U87)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U87)

(-) Exons   (0, 0)

(no "Exon" information available for 4U87)

(-) 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:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhh..hhhhhhhh....eee..........eeeeeeeeeeehhhhhhhhhhhhhh......eee..hhhhhhhhhhh.hhhhhhh.....hhhhheee...hhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u87 A   3 KEKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKR 203
                                    12        22        32        42|       62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 
                                                                  42|                                                                                                                                                      
                                                                   53                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhh..hhhhhhhh....eee....................eeeeeeeeeeehhhhhhhhhhhhhh......eee..hhhhhhhhhhh.hhhhhhh.....hhhhheee...hhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u87 B   3 KEKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKR 203
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 


Chain C from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhh..hhhhhhhh....eee....................eeeeeeeeeeehhhhhhhhhhhhhh......eee..hhhhhhhhhhh.hhhhhhh.....hhhhheee...hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u87 C   3 KEKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKR 203
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4U87)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U87)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U87)

(-) Gene Ontology  (5, 5)

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  4u87
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 Related Entries

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UniProtKB/Swiss-Prot
        REPB_STRAG | P13921: 3dkx 3dky

(-) Related Entries Specified in the PDB File

3dkx 3dky