Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ROLR (NCGL1110) WITHOUT LIGAND
 
Authors :  D. F. Li, N. Zhang, Y. J. Hou, S. J. Liu, D. C. Wang
Date :  18 Nov 10  (Deposition) - 06 Jul 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Helix-Turn-Helix, All Alpha, Transcription, Transcription Regulation, Transcription Regulator, All Helix, Tetr Family, Transcriptional Repressor, Resorcinol Binding, Dna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. F. Li, N. Zhang, Y. J. Hou, Y. Huang, Y. Hu, Y. Zhang, S. J. Liu, D. C. Wan
Crystal Structures Of The Transcriptional Repressor Rolr Reveals A Novel Recognition Mechanism Between Inducer And Regulator.
Plos One V. 6 E1952 2011
PubMed-ID: 21559286  |  Reference-DOI: 10.1371/JOURNAL.PONE.0019529

(-) Compounds

Molecule 1 - BACTERIAL REGULATORY PROTEINS, TETR FAMILY
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CG1308, CGL1157, NCGL1110
    Organism Common: BREVIBACTERIUM FLAVUM
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 196627
    Strain: ATCC 13032
    Synonym: TRANSCRIPTIONAL REGULATOR

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3AQS)

(-) Sites  (0, 0)

(no "Site" information available for 3AQS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AQS)

(-) 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:185
 aligned with Q8NR95_CORGL | Q8NR95 from UniProtKB/TrEMBL  Length:229

    Alignment length:193
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
         Q8NR95_CORGL    32 RARLITSARTLMAERGVDNVGIAEITEGANIGTGTFYNYFPDREQLLQAVAEDAFESVGIALDQVLTKLDDPAEVFAGSLRHLVRHSLEDRIWGGFFIQMGAAHPVLMRILGPRARRDLLHGLETGRFTIEDLDLATTCTFGSLIAAIQMALSADQDSNDDKDQIFAAAMLRMVGVQAAEAREIASRPLPEIS 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.........hhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.--------....hhhhhhhhh..hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqs A  32 RARLITSARTLMAERGVDNVGIAEITEGANIGTGTFYNYFPDREQLLQAVAEDAFESVGIALDQVLTKLDDPAEVFAGSLRHLVRHSLEDRIWGGFFIQMGAAHPVLMRILGPRARRDLLHGLETGRFTIEDLDLATTCTFGSLIAAIQMALS--------KDQIFAAAMLRMVGVQAAEAREIASRPLPEIS 224
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  |      - |     201       211       221   
                                                                                                                                                                                  184      193                               


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with Q8NR95_CORGL | Q8NR95 from UniProtKB/TrEMBL  Length:229

    Alignment length:194
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
         Q8NR95_CORGL    31 TRARLITSARTLMAERGVDNVGIAEITEGANIGTGTFYNYFPDREQLLQAVAEDAFESVGIALDQVLTKLDDPAEVFAGSLRHLVRHSLEDRIWGGFFIQMGAAHPVLMRILGPRARRDLLHGLETGRFTIEDLDLATTCTFGSLIAAIQMALSADQDSNDDKDQIFAAAMLRMVGVQAAEAREIASRPLPEIS 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..--------hhhhhhhhhhhhhh...hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqs B  31 TRARLITSARTLMAERGVDNVGIAEITEGANIGTGTFYNYFPDREQLLQAVAEDAFESVGIALDQVLTKLDDPAEVFAGSLRHLVRHSLEDRIWGGFFIQMGAAHPVLMRILGPRARRDLLHGLETGRFTIEDLDLATTCTFGSLIAAIQMALS--------KDQIFAAAMLRMVGVQAAEAREIASRPLPEIS 224
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   |     -  |    200       210       220    
                                                                                                                                                                                   184      193                               


Chain C from PDB  Type:PROTEIN  Length:185
 aligned with Q8NR95_CORGL | Q8NR95 from UniProtKB/TrEMBL  Length:229

    Alignment length:193
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
         Q8NR95_CORGL    32 RARLITSARTLMAERGVDNVGIAEITEGANIGTGTFYNYFPDREQLLQAVAEDAFESVGIALDQVLTKLDDPAEVFAGSLRHLVRHSLEDRIWGGFFIQMGAAHPVLMRILGPRARRDLLHGLETGRFTIEDLDLATTCTFGSLIAAIQMALSADQDSNDDKDQIFAAAMLRMVGVQAAEAREIASRPLPEIS 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.......hhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.--------.hhhhhhhhhhhhh.hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqs C  32 RARLITSARTLMAERGVDNVGIAEITEGANIGTGTFYNYFPDREQLLQAVAEDAFESVGIALDQVLTKLDDPAEVFAGSLRHLVRHSLEDRIWGGFFIQMGAAHPVLMRILGPRARRDLLHGLETGRFTIEDLDLATTCTFGSLIAAIQMALS--------KDQIFAAAMLRMVGVQAAEAREIASRPLPEIS 224
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  |      - |     201       211       221   
                                                                                                                                                                                  184      193                               


Chain D from PDB  Type:PROTEIN  Length:186
 aligned with Q8NR95_CORGL | Q8NR95 from UniProtKB/TrEMBL  Length:229

    Alignment length:194
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
         Q8NR95_CORGL    31 TRARLITSARTLMAERGVDNVGIAEITEGANIGTGTFYNYFPDREQLLQAVAEDAFESVGIALDQVLTKLDDPAEVFAGSLRHLVRHSLEDRIWGGFFIQMGAAHPVLMRILGPRARRDLLHGLETGRFTIEDLDLATTCTFGSLIAAIQMALSADQDSNDDKDQIFAAAMLRMVGVQAAEAREIASRPLPEIS 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh......hhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.--------hhhhhhhhhhhh......hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqs D  31 TRARLITSARTLMAERGVDNVGIAEITEGANIGTGTFYNYFPDREQLLQAVAEDAFESVGIALDQVLTKLDDPAEVFAGSLRHLVRHSLEDRIWGGFFIQMGAAHPVLMRILGPRARRDLLHGLETGRFTIEDLDLATTCTFGSLIAAIQMALS--------KDQIFAAAMLRMVGVQAAEAREIASRPLPEIS 224
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   |     -  |    200       210       220    
                                                                                                                                                                                   184      193
   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  (0, 0)

(no "SCOP Domain" information available for 3AQS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8NR95_CORGL | Q8NR95)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    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 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
(no "Ligands, Modified Residues, Ions" information available for 3aqs)
 
  Sites
(no "Sites" information available for 3aqs)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3aqs)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  3aqs
    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
  Q8NR95_CORGL | Q8NR95
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q8NR95_CORGL | Q8NR95
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8NR95_CORGL | Q8NR95: 3aqt

(-) Related Entries Specified in the PDB File

3aqt