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(-) Description

Title :  CCDBVFI:GYRA14EC
 
Authors :  N. De Jonge, R. 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) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
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 363-497
    Gene: GYRA, GYRASE, S2444, SF2311
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623
    Strain: K12
    Synonym: GYRA14
 
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
    Organism Scientific: ALIIVIBRIO FISCHERI
    Organism Taxid: 668

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:371 , HOH A:686 , ILE C:60 , ASP C:61 , ASN C:85 , HOH C:218BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREARG A:444BINDING SITE FOR RESIDUE CL A 502
3AC3SOFTWAREARG B:371 , HOH D:319BINDING SITE FOR RESIDUE CL D 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:492 -Gly A:493
2Gly B:493 -Ser B:494

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ELY)

(-) 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:135
                                                                                                                                                                       
               SCOP domains d4elya_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.ee..hhhhhhh................eee..eee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ely A 363 TRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADR 497
                                   372       382       392       402       412       422       432       442       452       462       472       482       492     


Chain B from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains d4elyb_ B: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.ee..hhhhhhhhh..............eee..eee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ely B 363 TRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADR 497
                                   372       382       392       402       412       422       432       442       452       462       472       482       492     


Chain C from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains d4elyc_ C: CcdB                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhh...eeee..hhhhh...eeeeeeeee........eeee..eeeee.hhhheeee.hhh..eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4ely C   2 SQFTLYKNKDKSSAKTYPYFVDVQSDLLDNLNTRLVIPLTPIEPSHLCPTIHIDEGDFIMLTQQMTSVPVKILSEPVNELSTFRNEIIAAIDFLITGI 105
                                    11        21        31        41  ||    57        67        77        87        97        
                                                                     44|                                                      
                                                                      51                                                      


Chain D from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains d4elyd_ D: CcdB                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........eeee..hhhhh...eeeeeeeee........eeee..eeeee.hhhheeee.hhh..eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4ely D   2 SQFTLYKNKDKSSAKTYPYFVDVQSDLLDNLNTRLVIPLTPIEPSHLCPTIHIDEGDFIMLTQQMTSVPVKILSEPVNELSTFRNEIIAAIDFLITGI 105
                                    11        21        31        41  ||    57        67        77        87        97        
                                                                     44|                                                      
                                                                      51
   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  (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 4ELY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 39)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly B:493 - Ser B:494   [ RasMol ]  
    Leu A:492 - Gly A:493   [ RasMol ]  
 

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  4ely
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
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  GYRA_ECOLI | P0AES4
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  GYRA_SHIFL | P0AES5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q84B82_ALIFS | Q84B82
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  5.99.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRA_ECOLI | P0AES4: 1ab4 1x75 1zi0 2y3p 3nuh
        GYRA_SHIFL | P0AES5: 1ab4 1x75 1zi0 2y3p 4ckk 4ckl
UniProtKB/TrEMBL
        Q84B82_ALIFS | Q84B82: 2kmt 3jrz 3jsc 3tcj

(-) Related Entries Specified in the PDB File

3jrz CCDBVFI-FORMII-PH5.6
3jsc CCDBVFI-FORMI-PH7.0
4elz