Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 PHIH1 REPRESSOR-LIKE PROTEIN FROM HALOARCULA MARISMORTUI
 
Authors :  Y. Kim, M. Zhou, L. Keigher, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  30 Oct 07  (Deposition) - 13 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Winged-Helix-Turn-Helix, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Zhou, L. Keigher, A. Joachimiak
Crystal Structure Of The Phih1 Repressor-Like Protein From Haloarcula Marismortui.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHIH1 REPRESSOR-LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PHRH2, RRNAC2285
    Organism Scientific: HALOARCULA MARISMORTUI ATCC 43049
    Organism Taxid: 272569
    Strain: DSM 3752, JCM 8966

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:37 , ILE B:38 , SER B:39 , SER B:42 , LYS B:82BINDING SITE FOR RESIDUE SO4 B 109
2AC2SOFTWAREARG A:37 , ILE A:38 , SER A:39 , SER A:42 , LYS A:82 , ARG B:37BINDING SITE FOR RESIDUE SO4 A 109

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B73)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B73)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B73)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B73)

(-) Exons   (0, 0)

(no "Exon" information available for 3B73)

(-) 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:88
 aligned with Q5V043_HALMA | Q5V043 from UniProtKB/TrEMBL  Length:108

    Alignment length:88
                              1                                                                                     
                              |      8        18        28        38        48        58        68        78        
          Q5V043_HALMA    - --MRQSGSWMTIWDDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPLANGVYVITEEGEAYLNGEYDAGKERYI 86
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b73A00 A:-1-86 'winged helix' repressor DNA binding domain                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhh..ee....ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  3b73 A -1 NAmRQSGSWmTIWDDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPLANGVYVITEEGEAYLNGEYDAGKERYI 86
                              |      8        18        28        38        48        58        68        78        
                              |      8-MSE                                                                          
                              1-MSE                                                                                 


Chain B from PDB  Type:PROTEIN  Length:89
 aligned with Q5V043_HALMA | Q5V043 from UniProtKB/TrEMBL  Length:108

    Alignment length:89
                              1                                                                                      
                              |      8        18        28        38        48        58        68        78         
          Q5V043_HALMA    - --MRQSGSWMTIWDDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPLANGVYVITEEGEAYLNGEYDAGKERYIN 87
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b73B00 B:-1-87 'winged helix' repressor DNA binding domain                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhheehhhhhhh......hhhhhhhhhhhhhhh..eeeehhheeeehhhhhhhhh..ee....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  3b73 B -1 NAmRQSGSWmTIWDDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPLANGVYVITEEGEAYLNGEYDAGKERYIN 87
                              |      8        18        28        38        48        58        68        78         
                              1-MSE  8-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  (0, 0)

(no "SCOP Domain" information available for 3B73)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B73)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3B73)

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3b73)
 

(-) 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
  3b73
    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
  Q5V043_HALMA | Q5V043
    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
  Q5V043_HALMA | Q5V043
    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 3B73)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3B73)