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(-) Description

Title :  CRYSTAL STRUCTURE OF PRIMASE REPB'
 
Authors :  S. Geibel, S. Banchenko, M. Engel, E. Lanka, W. Saenger
Date :  14 Apr 09  (Deposition) - 28 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Primase, Nucleotidyltransferase, Helix-Bundle-Domain, Replication, Rsf1010 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Geibel, S. Banchenko, M. Engel, E. Lanka, W. Saenger
Structure And Function Of Primase Repb' Encoded By Broad-Host-Range Plasmid Rsf1010 That Replicates Exclusivel In Leading-Strand Mode
Proc. Natl. Acad. Sci. Usa V. 106 7810 2009
PubMed-ID: 19416864  |  Reference-DOI: 10.1073/PNAS.0902910106

(-) Compounds

Molecule 1 - REPLICATION PROTEIN B
    Chains: A
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMS4708
    Expression System Strain: SCS1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: REPB
    Organism Scientific: PLASMID RSF1010
    Organism Taxid: 2504

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1DPO1Ligand/IonDIPHOSPHATE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1DPO1Ligand/IonDIPHOSPHATE
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1DPO2Ligand/IonDIPHOSPHATE
2SO46Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:110 , LYS A:174 , THR A:175 , HOH A:436BINDING SITE FOR RESIDUE SO4 A 324
2AC2SOFTWAREARG A:37 , TRP A:39 , ARG A:285 , LYS A:289 , HOH A:421BINDING SITE FOR RESIDUE SO4 A 325
3AC3SOFTWAREARG A:27 , GLY A:121 , ARG A:125 , ASP A:139 , SER A:140BINDING SITE FOR RESIDUE SO4 A 326
4AC4SOFTWARETYR A:62 , ARG A:145 , ASN A:151 , LYS A:153 , HOH A:535 , HOH A:565BINDING SITE FOR RESIDUE DPO A 327

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H20)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H20)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H20)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H20)

(-) Exons   (0, 0)

(no "Exon" information available for 3H20)

(-) 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:288
 aligned with Q52349_ECOLX | Q52349 from UniProtKB/TrEMBL  Length:323

    Alignment length:303
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   
         Q52349_ECOLX     5 RTLQAIGRQLKAMGCERFDIGVRDATTGQMMNREWSAAEVLQNTPWLKRMNAQGNDVYIRPAEQERHGLVLVDDLSEFDLDDMKAEGREPALVVETSPKNYQAWVKVADAAGGELRGQIARTLASEYDADPASADSRHYGRLAGFTNRKDKHTTRAGYQPWVLLRESKGKTATAGPALVQQAGQQIEQAQRQQEKARRLASLELPERQLSRHRRTALDEYRSEMAGLVKRFGDDLSKCDFIAAQKLASRGRSAEEIGKAMAEASPALAERKPGHEADYIERTVSKVMGLPSVQLARAELARAP 307
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhh.eeeeeee.......eeeeeeehhhhhhhhhhh.....eeeeee..eeeeeee.....hhhhhhhhhhhhhhhh..hhhhh.....ee........-....---.....eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..--hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h20 A   5 RTLQAIGRQLKAMGCERFDIGVRDATTGQMMNREWSAAEVLQNTPWLKRMNAQGNDVYIRPAEQERHGLVLVDDLSEFDLDDMKAEGREPALVVETSPKNYQAWVKVADAAGGELRGQIARTLASEYDADPASADSRHYGRLAGFTNRK-KHTT---YQPWVLLRESKGKTATAGPALVQQAGQQIEQAQRQQEKARRLASLE---------RRTALDEYRSEMAGLVKRFGDDLSKCDFIAAQKLASRGRSAEEIGKAMAEASPALAERK--HEADYIERTVSKVMGLPSVQLARAELARAP 307
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144        |-|  |   164       174       184       194       204  |      -  |    224       234       244       254       264       274|  |   284       294       304   
                                                                                                                                                                              153 |  | 162                                          207       217                                                       275  |                             
                                                                                                                                                                                155  |                                                                                                                     278                             
                                                                                                                                                                                   158
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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 3H20)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H20)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H20)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3H20)

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  3h20
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 Related Entries

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

UniProtKB/TrEMBL
        Q52349_ECOLX | Q52349: 3h25

(-) Related Entries Specified in the PDB File

3h25