Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS REGULATORY PROTEIN GERE
 
Authors :  V. M. -A. Ducros, R. J. Lewis, C. S. Verma, E. J. Dodson, G. Leonard, J. P. Turkenburg, G. N. Murshudov, A. J. Wilkinson, J. A. Brannigan
Date :  08 Sep 00  (Deposition) - 21 Mar 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,F  (1x)
Biol. Unit 3:  D,E  (1x)
Keywords :  Helix-Turn-Helix Dna-Binding Protein Transcriptional Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. M. Ducros, R. J. Lewis, C. S. Verma, E. J. Dodson, G. Leonard, J. P. Turkenburg, G. N. Murshudov, A. J. Wilkinson, J. A. Brannigan
Crystal Structure Of Gere, The Ultimate Transcriptional Regulator Of Spore Formation In Bacillus Subtilis.
J. Mol. Biol. V. 306 759 2001
PubMed-ID: 11243786  |  Reference-DOI: 10.1006/JMBI.2001.4443
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GERE
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   C  F
Biological Unit 3 (1x):    DE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:622 , HOH B:664 , ARG C:59 , SER C:60 , HOH C:527 , HOH C:560BINDING SITE FOR RESIDUE SO4 C 501
2AC2SOFTWARESER B:39 , THR B:42 , LYS C:41 , ARG C:44 , HOH C:525 , THR D:13 , ASN D:49 , LYS D:53 , GOL D:601 , HOH D:669BINDING SITE FOR RESIDUE SO4 C 502
3AC3SOFTWARESER A:39 , THR A:42 , HOH A:76 , THR C:13 , ASN C:49 , LYS C:53 , LYS D:41 , ARG D:44 , HOH D:614 , HOH D:620BINDING SITE FOR RESIDUE SO4 D 503
4AC4SOFTWAREARG D:59 , SER D:60 , HOH D:622 , HOH D:642BINDING SITE FOR RESIDUE SO4 D 504
5AC5SOFTWARETHR C:13 , LYS C:14 , ARG C:15 , ARG F:17 , GLU F:21 , HOH F:601BINDING SITE FOR RESIDUE GOL F 600
6AC6SOFTWAREPHE B:37 , ILE B:38 , SER B:39 , THR B:42 , ARG C:44 , SO4 C:502 , HOH C:520 , ASN D:49 , GLN D:52 , LYS D:53BINDING SITE FOR RESIDUE GOL D 601
7AC7SOFTWARELYS B:14 , ARG B:17 , GLU B:18 , HOH B:630 , HOH B:662BINDING SITE FOR RESIDUE GOL B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FSE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FSE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FSE)

(-) PROSITE Motifs  (2, 7)

Asymmetric Unit (2, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LUXR_2PS50043 LuxR-type HTH domain profile.GERE_BACSU5-70  1B:5-70
2HTH_LUXR_1PS00622 LuxR-type HTH domain signature.GERE_BACSU26-53
 
 
 
 
 		  6A:26-53
B:26-53
C:26-53
D:26-53
E:26-53
F:26-53
Biological Unit 1 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LUXR_2PS50043 LuxR-type HTH domain profile.GERE_BACSU5-70  1B:5-70
2HTH_LUXR_1PS00622 LuxR-type HTH domain signature.GERE_BACSU26-53
 
 
 
 
 		  2A:26-53
B:26-53
-
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LUXR_2PS50043 LuxR-type HTH domain profile.GERE_BACSU5-70  0-
2HTH_LUXR_1PS00622 LuxR-type HTH domain signature.GERE_BACSU26-53
 
 
 
 
 		  2-
-
C:26-53
-
-
F:26-53
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LUXR_2PS50043 LuxR-type HTH domain profile.GERE_BACSU5-70  0-
2HTH_LUXR_1PS00622 LuxR-type HTH domain signature.GERE_BACSU26-53
 
 
 
 
 		  2-
-
-
D:26-53
E:26-53
-

(-) Exons   (0, 0)

(no "Exon" information available for 1FSE)

(-) 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:67
 aligned with GERE_BACSU | P11470 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:67
                                    17        27        37        47        57        67       
            GERE_BACSU    8 SKPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
               SCOP domains d1fsea_ A: Germination protein GerE                                 SCOP domains
               CATH domains 1fseA00 A:8-74 'winged helix' repressor DNA binding domain          CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_LUXR_2  PDB: - UniProt: 5-70                               ---- PROSITE (1)
                PROSITE (2) ------------------HTH_LUXR_1  PDB: A:26-53    --------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------- Transcript
                  1fse A  8 SKPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
                                    17        27        37        47        57        67       


Chain B from PDB  Type:PROTEIN  Length:70
 aligned with GERE_BACSU | P11470 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:70
                                    14        24        34        44        54        64        74
            GERE_BACSU    5 EFQSKPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
               SCOP domains d1fseb_ B: Germination protein GerE                                    SCOP domains
               CATH domains 1fseB00 B:5-74 'winged helix' repressor DNA binding domain             CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_LUXR_2  PDB: B:5-70 UniProt: 5-70                             ---- PROSITE (1)
                PROSITE (2) ---------------------HTH_LUXR_1  PDB: B:26-53    --------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------- Transcript
                  1fse B  5 EFQSKPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
                                    14        24        34        44        54        64        74


Chain C from PDB  Type:PROTEIN  Length:67
 aligned with GERE_BACSU | P11470 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:67
                                    17        27        37        47        57        67       
            GERE_BACSU    8 SKPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
               SCOP domains d1fsec_ C: Germination protein GerE                                 SCOP domains
               CATH domains 1fseC00 C:8-74 'winged helix' repressor DNA binding domain          CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_LUXR_2  PDB: - UniProt: 5-70                               ---- PROSITE (1)
                PROSITE (2) ------------------HTH_LUXR_1  PDB: C:26-53    --------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------- Transcript
                  1fse C  8 SKPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
                                    17        27        37        47        57        67       


Chain D from PDB  Type:PROTEIN  Length:66
 aligned with GERE_BACSU | P11470 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:66
                                    18        28        38        48        58        68      
            GERE_BACSU    9 KPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
               SCOP domains d1fsed_ D: Germination protein GerE                                SCOP domains
               CATH domains 1fseD00 D:9-74 'winged helix' repressor DNA binding domain         CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) HTH_LUXR_2  PDB: - UniProt: 5-70                              ---- PROSITE (1)
                PROSITE (2) -----------------HTH_LUXR_1  PDB: D:26-53    --------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------ Transcript
                  1fse D  9 KPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
                                    18        28        38        48        58        68      


Chain E from PDB  Type:PROTEIN  Length:64
 aligned with GERE_BACSU | P11470 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:64
                                    20        30        40        50        60        70    
            GERE_BACSU   11 LLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
               SCOP domains d1fsee_ E: Germination protein GerE                              SCOP domains
               CATH domains 1fseE00 E:11-74 'winged helix' repressor DNA binding domain      CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_LUXR_2  PDB: - UniProt: 5-70                            ---- PROSITE (1)
                PROSITE (2) ---------------HTH_LUXR_1  PDB: E:26-53    --------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------- Transcript
                  1fse E 11 LLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
                                    20        30        40        50        60        70    


Chain F from PDB  Type:PROTEIN  Length:50
 aligned with GERE_BACSU | P11470 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:65
                                    19        29        39        49        59        69     
            GERE_BACSU   10 PLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
               SCOP domains d1fsef_ F: Germina               tion protein GerE                SCOP domains
               CATH domains 1fseF00 F:10-74 'w               inged helix' repressor DNA bindi CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..---------------hhhhhhhhhhhhh..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_LUXR_2  PDB: - UniProt: 5-70                             ---- PROSITE (1)
                PROSITE (2) ----------------HTH_LUXR_1  PDB: F:26-53    --------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------- Transcript
                  1fse F 10 PLLTKREREVFELLVQDK---------------VRNHISNAMQKLGVKGRSQAVVELLRMGELEL 74
                                    19       | -         -   |    49        59        69     
                                            27              43
   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, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FSE)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (GERE_BACSU | P11470)
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
    GOL  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1fse)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  1fse
    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
  GERE_BACSU | P11470
    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
  GERE_BACSU | P11470
    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 1FSE)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1FSE)