Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI TRANSCRIPTIONAL REPRESSOR ASCG
 
Authors :  A. U. Singer, O. Kagan, E. Evdokimova, J. Osipiuk, A. Joachimiak, A. M. E A. Savchenko, Midwest Center For Structural Genomics (Mcsg)
Date :  21 Dec 07  (Deposition) - 22 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcriptional Repressor Structure Escherichia Coli, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna-Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. U. Singer, O. Kagan, E. Evdokimova, J. Osipiuk, A. M. Edwards, A. Joachimiak, A. Savchenko
Structure Of The E. Coli Transcriptional Repressor Ascg.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR ASCG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: P15TVLIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ASCG, B2714, JW5434
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: CRYPTIC ASC OPERON REPRESSOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
1FRU1Ligand/IonFRUCTOSE
2MSE18Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:28 , SER A:149 , SO4 A:802 , HOH A:823 , HOH A:847 , HOH A:893 , HOH A:922BINDING SITE FOR RESIDUE FRU A 701
2AC2SOFTWARELEU B:28 , TYR B:29 , ARG B:84 , TRP B:180BINDING SITE FOR RESIDUE NA B 601
3AC3SOFTWAREGLY B:31 , TYR B:82 , ARG B:84 , ASN B:106 , SER B:149 , THR B:151 , HOH B:830 , HOH B:858BINDING SITE FOR RESIDUE SO4 B 801
4AC4SOFTWARETYR A:82 , ARG A:84 , ARG A:107 , SER A:149 , PRO A:150 , THR A:151 , FRU A:701BINDING SITE FOR RESIDUE SO4 A 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1His A:166 -Gly A:167
2Val A:224 -Pro A:225
3Val A:243 -Pro A:244
4Val B:224 -Pro B:225
5Val B:243 -Pro B:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BRQ)

(-) 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:271
 aligned with ASCG_ECOLI | P24242 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:275
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328     
           ASCG_ECOLI    59 TQTLGLVVTNTLYHGIYFSELLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIYPRFLSVDEIDDIIDAHSQPIMVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSMDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEMLLERGAKFSALVASNDDMAIGAMKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEMIQEIIGRLIFMLDGGDFSPPKTFSGKLIRRDSLIA 333
               SCOP domains d3brqa_ A: aut  omated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -3brqA01 A:18-  119,A:251-280  [code=3.40.50.2300, no name defined]                                    3brqA02 A:120-250,A:281-291  [code=3.40.50.2300, no name defined]                                                                  3brqA01 A:18-119,A:251-280    3brqA02     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhh.--hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh....eeee......hhh.ee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh.....hhh.ee....hhhhhhhhhhhhhh.--...eeee.hhhhhhhhhhhhhhhh.......eeeee....hhhhh....eeee.hhhhhhhhhhhhhhhhhh............eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3brq A  17 TQTLGLVVTNTLYH--YFSELLFHAARmAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAImIYPRFLSVDEIDDIIDAHSQPImVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSmDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEmLLER--KFSALVASNDDmAIGAmKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEmIQEIIGRLIFmLDGGDFSPPKTFSGKLIRRDSLIA 291
                                    26   |  | 36       |46        56        66        76   |    86        96      |106       116       126       136       146|      156       166       176       186    |   |- |     206  |    216       226       236       246       256       266|      276       286     
                                        30 33         44-MSE                              80-MSE                103-MSE                                     147-MSE                                     191-MSE  |        209-MSE|                                       256-MSE    267-MSE                    
                                                                                                                                                                                                               198             214-MSE                                                                         


Chain B from PDB  Type:PROTEIN  Length:277
 aligned with ASCG_ECOLI | P24242 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:277
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       
           ASCG_ECOLI    59 TQTLGLVVTNTLYHGIYFSELLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIYPRFLSVDEIDDIIDAHSQPIMVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSMDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEMLLERGAKFSALVASNDDMAIGAMKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEMIQEIIGRLIFMLDGGDFSPPKTFSGKLIRRDSLIAPS 335
               SCOP domains d3brqb_ B: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -3brqB01 B:18-119,B:251-280  [code=3.40.50.2300, no name defined]                                      3brqB02 B:120-250,B:281-293  [code=3.40.50.2300, no name defined]                                                                  3brqB01 B:18-119,B:251-280    3brqB02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh....eeee......hhh.ee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhh....hhh.ee....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh........eeeee....hhhhh....eeee.hhhhhhhhhhhhhhhhhh............eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3brq B  17 TQTLGLVVTNTLYHGIYFSELLFHAARmAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAImIYPRFLSVDEIDDIIDAHSQPImVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSmDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEmLLERGAKFSALVASNDDmAIGAmKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEmIQEIIGRLIFmLDGGDFSPPKTFSGKLIRRDSLIAPS 293
                                    26        36       |46        56        66        76   |    86        96      |106       116       126       136       146|      156       166       176       186    |  196       206  |    216       226       236       246       256       266|      276       286       
                                                      44-MSE                              80-MSE                103-MSE                                     147-MSE                                     191-MSE           209-MSE|                                       256-MSE    267-MSE                      
                                                                                                                                                                                                                               214-MSE
   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, 2)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ASCG_ECOLI | P24242)
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.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FRU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:166 - Gly A:167   [ RasMol ]  
    Val A:224 - Pro A:225   [ RasMol ]  
    Val A:243 - Pro A:244   [ RasMol ]  
    Val B:224 - Pro B:225   [ RasMol ]  
    Val B:243 - Pro B:244   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3brq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ASCG_ECOLI | P24242
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ASCG_ECOLI | P24242
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ASCG_ECOLI | P24242: 3dbi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3BRQ)