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(-) Description

Title :  STRUCTURE OF PARB BOUND TO DNA
 
Authors :  M. A. Schumacher, B. E. Funnell
Date :  06 Jun 05  (Deposition) - 29 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.98
Chains :  Asym./Biol. Unit :  A,B,S,T
Keywords :  Partition; P1; Plasmid, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, B. E. Funnell
Structures Of Parb Bound To Dna Reveal Mechanism Of Partition Complex Formation.
Nature V. 438 516 2005
PubMed-ID: 16306995  |  Reference-DOI: 10.1038/NATURE04149
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PARS-SMALL DNA CENTROMERE SITE
    Chains: T
    Engineered: YES
    Other Details: W-STRAND
    Synthetic: YES
 
Molecule 2 - PARS-SMALL DNA CENTROMERE SITE
    Chains: S
    Engineered: YES
    Other Details: C-STRAND
    Synthetic: YES
 
Molecule 3 - PLASMID PARTITION PAR B PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: P1 PARB
    Gene: PARB
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE P1
    Organism Taxid: 10678
    Synonym: P1 PARB;
PARB

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABST

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:208 , ASP A:209 , LYS A:211 , THR A:212BINDING SITE FOR RESIDUE CIT A 1585
2AC2SOFTWARECYS A:214 , ALA A:215 , ASP A:218 , GLU A:219BINDING SITE FOR RESIDUE CIT A 1586

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZX4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZX4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZX4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZX4)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZX4)

(-) Sequences/Alignments

Asymmetric/Biological 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:180
 aligned with Q38420_BPP1 | Q38420 from UniProtKB/TrEMBL  Length:333

    Alignment length:181
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325 
          Q38420_BPP1   146 ALQHSIREIGLRLMRMKNDGMSQKDIAAKEGLSQAKVTRALQAASAPEELVALFPVQSELTFSDYKTLCAVGDEMGNKNLEFDQLIQNISPEINDILSIEEMAEDEVKNKILRLITKEASLLTDKGSKDKSVVTELWKFEDKDRFARKRVKGRAFSYEFNRLSKELQEELDRMIGHILRKS 326
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh-..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.......eeeeee...eeeeeee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zx4 A 146 ALQHSIREIGLRLmRmKNDGmSQKDIAAKEGLSQAKVTRALQAASAPEELVALFPVQSELTFSDYKTLCAVGDEmGNKNLEFDQLIQNISPEINDILSI-EmAEDEVKNKILRLITKEASLLTDKGSKDKSVVTELWKFEDKDRFARKRVKGRAFSYEFNRLSKELQEELDRmIGHILRKS 326
                                   155   | | 165|      175       185       195       205       215    |  225       235        |-||     255       265       275       285       295       305       315  |    325 
                                       159-MSE  |                                                   220-MSE                 244 ||                                                                    318-MSE    
                                         161-MSE|                                                                             246|                                                                               
                                              166-MSE                                                                          247-MSE                                                                           


Chain B from PDB  Type:PROTEIN  Length:176
 aligned with Q38420_BPP1 | Q38420 from UniProtKB/TrEMBL  Length:333

    Alignment length:179
                                   159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         
          Q38420_BPP1   150 SIREIGLRLMRMKNDGMSQKDIAAKEGLSQAKVTRALQAASAPEELVALFPVQSELTFSDYKTLCAVGDEMGNKNLEFDQLIQNISPEINDILSIEEMAEDEVKNKILRLITKEASLLTDKGSKDKSVVTELWKFEDKDRFARKRVKGRAFSYEFNRLSKELQEELDRMIGHILRKSLD 328
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------ParB-1zx4B01 B:199-325                                                                                                         --- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------ParB-1zx4B02 B:199-325                                                                                                         --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh...hhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...---..eeeeeee......eeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zx4 B 150 SIREIGLRLmRmKNDGmSQKDIAAKEGLSQAKVTRALQAASAPEELVALFPVQSELTFSDYKTLCAVGDEmGNKNLEFDQLIQNISPEINDILSINEmAEDEVKNKILRLITKEASLLTDKG---KSVVTELWKFEDKDRFARKRVKGRAFSYEFNRLSKELQEELDRmIGHILRKSLD 328
                                   159 |    |169       179       189       199       209       219|      229       239       249       259       269 |   | 279       289       299       309       319         
                                   159-MSE  |                                                   220-MSE                    247-MSE                 271 275                                        318-MSE      
                                     161-MSE|                                                                                                                                                                  
                                          166-MSE                                                                                                                                                              


Chain S from PDB  Type:DNA  Length:25
                                                         
                 1zx4 S   3 CGTGGCGATTTCACCTTGAAATCGC  27
                                    12        22     


Chain T from PDB  Type:DNA  Length:25
                                                         
                 1zx4 T  14 GCGATTTCAAGGTGAAATCGCCACG  38
                                    23        33
   Legend:   → Mismatch (orange background)
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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 1ZX4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZX4)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: ParB] (2)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q38420_BPP1 | Q38420)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

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 Related Entries

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

UniProtKB/TrEMBL
        Q38420_BPP1 | Q38420: 2ntz

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