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(-) Description

Title :  PARM WITH GMPPNP
 
Authors :  D. Popp, A. Narita, T. Oda, T. Fujisawa, H. Matsuo, Y. Nitanai, M. Iwasa, K. Maeda, H. Onishi, Y. Maeda
Date :  30 Jan 08  (Deposition) - 12 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Parm, Plasmid, Plasmid Partition, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Popp, A. Narita, T. Oda, T. Fujisawa, H. Matsuo, Y. Nitanai, M. Iwasa, K. Maeda, H. Onishi, Y. Maeda
Molecular Structure Of The Parm Polymer And The Mechanism Leading To Its Nucleotide-Driven Dynamic Instability
Embo J. V. 27 570 2008
PubMed-ID: 18188150  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601978
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASMID SEGREGATION PROTEIN PARM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMD137
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PROTEIN STBA, PARA LOCUS 36 KDA PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC3SOFTWAREGNP A:323 , HOH A:324 , HOH A:325 , HOH A:326 , HOH A:327BINDING SITE FOR RESIDUE MG A 321
2AC4SOFTWAREASP A:7 , GLN A:73 , THR A:101 , HOH A:328BINDING SITE FOR RESIDUE MG A 322
3AC5SOFTWAREGNP B:323 , HOH B:324 , HOH B:325 , HOH B:326 , HOH B:327BINDING SITE FOR RESIDUE MG B 321
4AC6SOFTWAREASP B:7 , GLN B:73 , THR B:101 , HOH B:328BINDING SITE FOR RESIDUE MG B 322
5AC7SOFTWAREGLY A:8 , SER A:9 , THR A:10 , ASN A:11 , LYS A:13 , GLY A:172 , GLY A:173 , THR A:174 , THR A:175 , ILE A:226 , GLY A:281 , GLU A:284 , LEU A:285 , GLN A:308 , MG A:321 , HOH A:326 , HOH A:331 , HOH A:334 , HOH A:355 , HOH A:374 , HOH A:416 , HOH A:449BINDING SITE FOR RESIDUE GNP A 323
6AC8SOFTWAREGLY B:8 , SER B:9 , THR B:10 , ASN B:11 , LYS B:13 , GLY B:172 , GLY B:173 , THR B:174 , THR B:175 , ILE B:226 , GLY B:281 , GLU B:284 , LEU B:285 , GLN B:308 , MG B:321 , HOH B:326 , HOH B:330 , HOH B:334 , HOH B:364 , HOH B:375 , HOH B:394 , HOH B:427BINDING SITE FOR RESIDUE GNP B 323

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZGZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZGZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZGZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZGZ)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZGZ)

(-) 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:320
 aligned with PARM_ECOLX | P11904 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:320
                                    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       300       310       320
           PARM_ECOLX     1 MLVFIDDGSTNIKLQWQESDGTIKQHISPNSFKREWAVSFGDKKVFNYTLNGEQYSFDPISPDAVVTTNIAWQYSDVNVVAVHHALLTSGLPVSEVDIVCTLPLTEYYDRNNQPNTENIERKKANFRKKITLNGGDTFTIKDVKVMPESIPAGYEVLQELDELDSLLIIDLGGTTLDISQVMGKLSGISKIYGDSSLGVSLVTSAVKDALSLARTKGSSYLADDIIIHRKDNNYLKQRINDENKISIVTEAMNEALRKLEQRVLNTLNEFSGYTHVMVIGGGAELICDAVKKHTQIRDERFFKTNNSQYDLVNGMYLIGN 320
               SCOP domains d2zgza1 A:1-157 Plasmid segregation protein ParM                                                                                                             d2zgza2 A:158-320 Plasmid segregation protein ParM                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeeee.....eeeeeee..ee.............eeee..eeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeehhhhhh......hhhhhhhhhhhh...eee......eeeeeeeee.hhhhhhhhhhhh....eeeeeee....eeeeeee.hhh.eeeeeee....hhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhh...hhh.ee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zgz A   1 MLVFIDDGSTNIKLQWQESDGTIKQHISPNSFKREWAVSFGDKKVFNYTLNGEQYSFDPISPDAVVTTNIAWQYSDVNVVAVHHALLTSGLPVSEVDIVCTLPLTEYYDRNNQPNTENIERKKANFRKKITLNGGDTFTIKDVKVMPESIPAGYEVLQELDELDSLLIIDLGGTTLDISQVMGKLSGISKIYGDSSLGVSLVTSAVKDALSLARTKGSSYLADDIIIHRKDNNYLKQRINDENKISIVTEAMNEALRKLEQRVLNTLNEFSGYTHVMVIGGGAELICDAVKKHTQIRDERFFKTNNSQYDLVNGMYLIGN 320
                                    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       300       310       320


Chain B from PDB  Type:PROTEIN  Length:320
 aligned with PARM_ECOLX | P11904 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:320
                                    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       300       310       320
           PARM_ECOLX     1 MLVFIDDGSTNIKLQWQESDGTIKQHISPNSFKREWAVSFGDKKVFNYTLNGEQYSFDPISPDAVVTTNIAWQYSDVNVVAVHHALLTSGLPVSEVDIVCTLPLTEYYDRNNQPNTENIERKKANFRKKITLNGGDTFTIKDVKVMPESIPAGYEVLQELDELDSLLIIDLGGTTLDISQVMGKLSGISKIYGDSSLGVSLVTSAVKDALSLARTKGSSYLADDIIIHRKDNNYLKQRINDENKISIVTEAMNEALRKLEQRVLNTLNEFSGYTHVMVIGGGAELICDAVKKHTQIRDERFFKTNNSQYDLVNGMYLIGN 320
               SCOP domains d2zgzb1 B:1-157 Plasmid segregation protein ParM                                                                                                             d2zgzb2 B:158-320 Plasmid segregation protein ParM                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) StbA-2zgzB01 B:1-318                                                                                                                                                                                                                                                                                                          -- Pfam domains (1)
           Pfam domains (2) StbA-2zgzB02 B:1-318                                                                                                                                                                                                                                                                                                          -- Pfam domains (2)
         Sec.struct. author .eeeeee...eeeeeee.....eeeeeee..ee.............eeee..eeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeehhhhhh......hhhhhhhhhhhh...eee......eeeeeeeee.hhhhhhhhhhhh....eeeeeee....eeeeeee.hhh.eeeeeee....hhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhh...hhh.ee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zgz B   1 MLVFIDDGSTNIKLQWQESDGTIKQHISPNSFKREWAVSFGDKKVFNYTLNGEQYSFDPISPDAVVTTNIAWQYSDVNVVAVHHALLTSGLPVSEVDIVCTLPLTEYYDRNNQPNTENIERKKANFRKKITLNGGDTFTIKDVKVMPESIPAGYEVLQELDELDSLLIIDLGGTTLDISQVMGKLSGISKIYGDSSLGVSLVTSAVKDALSLARTKGSSYLADDIIIHRKDNNYLKQRINDENKISIVTEAMNEALRKLEQRVLNTLNEFSGYTHVMVIGGGAELICDAVKKHTQIRDERFFKTNNSQYDLVNGMYLIGN 320
                                    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       300       310       320
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZGZ)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Actin_ATPase (173)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PARM_ECOLX | P11904)
biological process
    GO:0030541    plasmid partitioning    Any process in which plasmids are segregated or distributed into daughter cells upon cell division.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PARM_ECOLX | P11904: 1mwk 1mwm 2qu4 2zgy 2zhc 3iku 3iky 4a61 4a62 4a6j 5aey 5ai7

(-) Related Entries Specified in the PDB File

2zgy PARM WITH GDP