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(-) Description

Title :  CRYSTAL STRUCTURE OF MATP-MATS
 
Authors :  M. A. Schumacher
Date :  07 Jan 12  (Deposition) - 21 Nov 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,M,N
Biol. Unit 1:  A,B,M,N  (2x)
Keywords :  Macrodomains, Chromosome, Dna Condensation, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Dupaigne, N. K. Tonthat, O. Espeli, T. Whitfill, F. Boccard, M. A. Schumacher
Molecular Basis For A Protein-Mediated Dna-Bridging Mechanism That Functions In Condensation Of The E. Coli Chromosome.
Mol. Cell V. 48 560 2012
PubMed-ID: 23084832  |  Reference-DOI: 10.1016/J.MOLCEL.2012.09.009

(-) Compounds

Molecule 1 - MACRODOMAIN TER PROTEIN
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MATP, YPO1433, Y2737, YP_0877
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: MATP
 
Molecule 2 - 5'-D(*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*G)-3'
    Chains: N
    Engineered: YES
    Other Details: MATS STRAND 2
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*G)-3'
    Chains: M
    Engineered: YES
    Other Details: MATS STRAND 1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABMN
Biological Unit 1 (2x): ABMN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG M:16 , DG N:3BINDING SITE FOR RESIDUE CA N 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VEB)

(-) 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:146
 aligned with MATP_YERPE | Q8ZG78 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
           MATP_YERPE     2 KYQQLENLESGWKWAYLVKKHREGEAITRHIENSAAQDAVEQLMKLENEPVKVQEWIDAHMNVNLATRMKQTIRARRKRHFNAEHQHTRKKSIDLEFLVWQRLAVLARRRGNTLSDTVVQLIEDAERKEKYASQMSSLKQDLKDIL 147
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3veb A  15 KYQQLENLESGWKWAYLVKKHREGEAITRHIENSAAQDAVEQLMKLENEPVKVQEWIDAHMNVNLATRMKQTIRARRKRHFNAEHQHTRKKSIDLEFLVWQRLAVLARRRGNTLSDTVVQLIEDAERKEKYASQMSSLKQDLKDIL 160
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154      


Chain B from PDB  Type:PROTEIN  Length:150
 aligned with MATP_YERPE | Q8ZG78 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
           MATP_YERPE     1 MKYQQLENLESGWKWAYLVKKHREGEAITRHIENSAAQDAVEQLMKLENEPVKVQEWIDAHMNVNLATRMKQTIRARRKRHFNAEHQHTRKKSIDLEFLVWQRLAVLARRRGNTLSDTVVQLIEDAERKEKYASQMSSLKQDLKDILDKE 150
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......eee...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3veb B  14 MKYQQLENLESGWKWAYLVKKHREGEAITRHIENSAAQDAVEQLMKLENEPVKVQEWIDAHMNVNLATRMKQTIRARRKRHFNAEHQHTRKKSIDLEFLVWQRLAVLARRRGNTLSDTVVQLIEDAERKEKYASQMSSLKQDLKDILDKE 163
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163


Chain M from PDB  Type:DNA  Length:16
                                                
                 3veb M   1 ACGTGACAATGTCACG  16
                                    10      


Chain N from PDB  Type:DNA  Length:16
                                                
                 3veb N   1 TCGTGACATTGTCACG  16
                                    10
   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 3VEB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MATP_YERPE | Q8ZG78)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MATP_YERPE | Q8ZG78: 3vea

(-) Related Entries Specified in the PDB File

3vea 4d8j