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(-) Description

Title :  CCDBVFI:GYRA14VFI
 
Authors :  N. De Jonge, M. Simic, L. Buts, S. Haesaerts, K. Roelants, A. Garcia-Pi Y. Sterckx, H. De Greve, J. Lah, R. Loris
Date :  11 Apr 12  (Deposition) - 30 May 12  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha+Beta, Topoisomerase, Toxin-Isomerase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. De Jonge, M. Simic, L. Buts, S. Haesaerts, K. Roelants, A. Garcia-Pino, Y. Sterckx, H. De Greve, J. Lah, R. Loris
Alternative Interactions Define Gyrase Specificity In The Ccdb Family.
Mol. Microbiol. V. 84 965 2012
PubMed-ID: 22582791  |  Reference-DOI: 10.1111/J.1365-2958.2012.08069.X

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT A
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 362-493
    Gene: GYRA, VF_1204
    Organism Scientific: VIBRIO FISCHERI
    Organism Taxid: 312309
    Strain: ATCC 700601 / ES114
 
Molecule 2 - CCDB
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Strain: B462
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CCDB, VFMJ11_A0651
    Organism Scientific: VIBRIO FISCHERI
    Organism Taxid: 388396
    Strain: MJ11

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:374 , ALA A:377 , HIS A:378 , GLU A:381 , THR A:429 , ALA A:432 , ARG A:433 , PRO A:434BINDING SITE FOR RESIDUE GOL A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu B:445 -Gly B:446

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ELZ)

(-) 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:143
                                                                                                                                                                               
               SCOP domains d4elza_ A: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhh.........eee..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4elz A 352 SSGLVPRGSHMTRRTIFELRKARDRAHILEGLALALANIDEIIELIKNAPTPAEAKEGLISRGWDLGNVASMLERAGTDAARPDWLEPEFGIREGKYFLTEQQAQAILELRLHRLTGLEHEKILDEYKALLDEIAELMHILAS 494
                                   361       371       381       391       401       411       421       431       441       451       461       471       481       491   


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains d4elzb_ B: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhh..ee...hhhhhhhhhhh...........eee..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4elz B 362 MTRRTIFELRKARDRAHILEGLALALANIDEIIELIKNAPTPAEAKEGLISRGWDLGNVASMLERAGTDAARPDWLEPEFGIREGKYFLTEQQAQAILELRLHRLTGLEHEKILDEYKALLDEIAELMHIL 492
                                   371       381       391       401       411       421       431       441       451       461       471       481       491 


Chain C from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains d4elzc_ C: CcdB                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........eeee..hhhhh...eeeeeeeee.hhh..........eeee..eeeee.hhhheeee.hhh..eeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4elz C   2 SQFTLYKNKDKSSAKTYPYFVDVQSDLLDNLNTRLVIPLTPIELLDKKAPSHLCPTIHIDEGDFIMLTQQMTSVPVKILSEPVNELSTFRNEIIAAIDFLITGI 105
                                    11        21        31        41        51        61        71        81        91       101    


Chain D from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains d4elzd_ D: CcdB                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...........eeee..hhhhh...eeeeeeeee.hhh........eeee..eeeee.hhhheeee.hhhh.eeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4elz D   2 SQFTLYKNKDKSSAKTYPYFVDVQSDLLDNLNTRLVIPLTPIELLKAPSHLCPTIHIDEGDFIMLTQQMTSVPVKILSEPVNELSTFRNEIIAAIDFLITGI 105
                                    11        21        31        41    ||  53        63        73        83        93       103  
                                                                       46|                                                        
                                                                        49
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu B:445 - Gly B:446   [ RasMol ]  
 

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3jrz CCDBVFI-FORMII-PH5.6
3jsc CCDBVFI-FORMI-PH7.0