Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 BACTERIAL REGULATORY PROTEIN OF GNTR FAMILY FROM CORYNEBACTERIUM GLUTAMICUM
 
Authors :  R. Zhang, M. Zhou, M. Gu, A. Joachimiak, Midwest Center For Structur Genomics (Mcsg)
Date :  02 Mar 07  (Deposition) - 22 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Keywords :  Bacterial Regulatory Protein, Gntr Family, Mcsg, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, M. Zhou, M. Gu, A. Joachimiak
The Crystal Structure Of Bacterial Regulatory Protein Of Gntr Family From Corynebacterium Glutamicum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Atcc: 13032
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 105-253
    Gene: CGL0157, CG0196
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Strain: DSM 20300, JCM 1318, LMG 3730, NCIMB 10025
    Synonym: BACTERIAL REGULATORY PROTEIN, GNTR FAMILY

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (2x):  B 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2P19)

(-) Sites  (0, 0)

(no "Site" information available for 2P19)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P19)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P19)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P19)

(-) Exons   (0, 0)

(no "Exon" information available for 2P19)

(-) 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:148
 aligned with Q8NTZ4_CORGL | Q8NTZ4 from UniProtKB/TrEMBL  Length:253

    Alignment length:148
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245        
         Q8NTZ4_CORGL   106 KNANLDPKTRVLEHRLLAASSAIAEKLGVSAGDEVLLIRRLRSTGDIPVAILENYLPPAFNDVSLDELEKGGLYDALRSRGVVLKIANQKIGARRAVGEESTLLDIEDGGPLLTVERVALDNSGQVIELGSHCYRPDMYNFETTLVAR 253
               SCOP domains d2p19a1 A:2-149 Transcriptional regulator Cgl0157/Cg0196                                                                                             SCOP domains
               CATH domains -----2p19A01 A:7-136 Chorismate lyase                                                                                                  ------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee..eeeeeeeeeehhhhh..hhhhhhhhhhhhhhhhh.....eeeeeeeeee...hhhhhhh.....eeeeeeeeee.....eeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p19 A   2 KNANLDPKTRVLEHRLLAASSAIAEKLGVSAGDEVLLIRRLRSTGDIPVAILENYLPPAFNDVSLDELEKGGLYDALRSRGVVLKIANQKIGARRAVGEESTLLDIEDGGPLLTVERVALDNSGQVIELGSHCYRPDMYNFETTLVAR 149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        


Chain B from PDB  Type:PROTEIN  Length:142
 aligned with Q8NTZ4_CORGL | Q8NTZ4 from UniProtKB/TrEMBL  Length:253

    Alignment length:142
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250  
         Q8NTZ4_CORGL   111 DPKTRVLEHRLLAASSAIAEKLGVSAGDEVLLIRRLRSTGDIPVAILENYLPPAFNDVSLDELEKGGLYDALRSRGVVLKIANQKIGARRAVGEESTLLDIEDGGPLLTVERVALDNSGQVIELGSHCYRPDMYNFETTLVA 252
               SCOP domains d2p19b_ B: Transcriptional regulator Cgl0157/Cg0196                                                                                            SCOP domains
               CATH domains 2p19B01 B:7-136 Chorismate lyase                                                                                                  ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee..eeeeeeeeeehhhhh..hhhhhhhhhhhhhhhhh.....eeeeeeeeee...hhhhhh......eeeeeeeeee.....eeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p19 B   7 DPKTRVLEHRLLAASSAIAEKLGVSAGDEVLLIRRLRSTGDIPVAILENYLPPAFNDVSLDELEKGGLYDALRSRGVVLKIANQKIGARRAVGEESTLLDIEDGGPLLTVERVALDNSGQVIELGSHCYRPDMYNFETTLVA 148
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146  


Chain C from PDB  Type:PROTEIN  Length:148
 aligned with Q8NTZ4_CORGL | Q8NTZ4 from UniProtKB/TrEMBL  Length:253

    Alignment length:148
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244        
         Q8NTZ4_CORGL   105 LKNANLDPKTRVLEHRLLAASSAIAEKLGVSAGDEVLLIRRLRSTGDIPVAILENYLPPAFNDVSLDELEKGGLYDALRSRGVVLKIANQKIGARRAVGEESTLLDIEDGGPLLTVERVALDNSGQVIELGSHCYRPDMYNFETTLVA 252
               SCOP domains d2p19c_ C: Transcriptional regulator Cgl0157/Cg0196                                                                                                  SCOP domains
               CATH domains ------2p19C01 C:7-136 Chorismate lyase                                                                                                  ------------ CATH domains
           Pfam domains (1) --UTRA-2p19C01 C:3-141                                                                                                                       ------- Pfam domains (1)
           Pfam domains (2) --UTRA-2p19C02 C:3-141                                                                                                                       ------- Pfam domains (2)
           Pfam domains (3) --UTRA-2p19C03 C:3-141                                                                                                                       ------- Pfam domains (3)
         Sec.struct. author hhhhhhheeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee..eeeeeeeeeehhhhh..hhhhhhhhhhhhhhhh......eeeeeeeeee...hhhhhhh.....eeeeeeeeee.....eeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p19 C   1 LKNANLDPKTRVLEHRLLAASSAIAEKLGVSAGDEVLLIRRLRSTGDIPVAILENYLPPAFNDVSLDELEKGGLYDALRSRGVVLKIANQKIGARRAVGEESTLLDIEDGGPLLTVERVALDNSGQVIELGSHCYRPDMYNFETTLVA 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Chor_lyase (11)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8NTZ4_CORGL | Q8NTZ4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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 2p19)
 
  Sites
(no "Sites" information available for 2p19)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2p19)
 
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
  2p19
    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
  Q8NTZ4_CORGL | Q8NTZ4
    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
  Q8NTZ4_CORGL | Q8NTZ4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2P19)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2P19)