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(-) Description

Title :  CRYSTAL STRUCTURE OF DEGV, A FATTY ACID BINDING PROTEIN FROM BACILLUS SUBTILIS
 
Authors :  J. Nan, Y. F. Zhou, C. Yang
Date :  23 Jan 09  (Deposition) - 12 May 09  (Release) - 12 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Fatty Acid-Binding, Edd Fold, Fatty Acid-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Nan, Y. F. Zhou, C. Yang, E. Brostromer, O. Kristensen, X. -D. Su
Structure Of A Fatty Acid-Binding Protein From Bacillus Subtilis Determined By Sulfur-Sad Phasing Using In-House Chromium Radiation
Acta Crystallogr. , Sect. D V. 65 440 2009
PubMed-ID: 19390149  |  Reference-DOI: 10.1107/S0907444909007756
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DEGV
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BSU35480, DEGV, YVIA
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1BR7Ligand/IonBROMIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3PLM1Ligand/IonPALMITIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:61 , SER A:62 , GLN A:63 , ILE A:92 , SER A:93 , ARG A:172 , ILE A:197 , ILE A:232 , HIS A:268 , GLY A:275 , ILE A:276 , HOH A:290 , HOH A:302BINDING SITE FOR RESIDUE PLM A 501
2AC2SOFTWAREARG A:156 , ALA A:157 , PHE A:192BINDING SITE FOR RESIDUE EDO A 601
3AC3SOFTWARESER A:175BINDING SITE FOR RESIDUE BR A 701
4AC4SOFTWAREMET A:160 , HOH A:308BINDING SITE FOR RESIDUE BR A 702
5AC5SOFTWAREASP A:103 , VAL A:106 , ILE A:109 , ASP A:110BINDING SITE FOR RESIDUE BR A 703
6AC6SOFTWAREGLY A:77 , TYR A:80 , ASN A:108 , HOH A:287 , HOH A:379BINDING SITE FOR RESIDUE BR A 704
7AC7SOFTWAREALA A:138BINDING SITE FOR RESIDUE BR A 705
8AC8SOFTWAREARG A:18BINDING SITE FOR RESIDUE BR A 706
9AC9SOFTWAREASP A:163 , LEU A:164BINDING SITE FOR RESIDUE BR A 707

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEGVPS51482 DegV domain profile.DEGV_BACSU3-280  1A:3-280

(-) Exons   (0, 0)

(no "Exon" information available for 3FYS)

(-) 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:282
 aligned with DEGV_BACSU | P32436 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:282
                             1                                                                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279  
           DEGV_BACSU     - -MNIAVVTDSTAYIPKEMREQHQIHMIPLQVVFREETYREEIELDWKSFYEEVKKHNELPTTSQPPIGELVALYEELGKSYDAVISIHLSSGISGTFSSAAAADSMVDNIDVYPFDSEISCLAQGFYALKAAELIKNGASSPEDIIKELEEMKKTVRAYFMVDDLAHLQRGGRLSSAQAFIGSLLKVKPILHFDNKVIVPFEKIRTRKKAISRIYELLDEDASKGLPMRAAVIHANREEEAAKIIEELSAKYPHVEFYNSYFGAVIGTHLGEGALGICWCFK 281
               SCOP domains d3fysa_ A: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------3fysA02 A:153-281  [code=3.30.1180.10, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.hhh.hhhhhhhhheeee..eee....eee.....hhhhhhhhhhh.....eee..hhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...eeeee...hhhhhhhh.hhhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---DEGV  PDB: A:3-280 UniProt: 3-280                                                                                                                                                                                                                                                     - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fys A   0 SMNIAVVTDSTAYIPKEMREQHQIHMIPLQVVFREETYREEIELDWKSFYEEVKKHNELPTTSQPPIGELVALYEELGKSYDAVISIHLSSGISGTFSSAAAADSMVDNIDVYPFDSEISCLAQGFYALKAAELIKNGASSPEDIIKELEEMKKTVRAYFMVDDLAHLQRGGRLSSAQAFIGSLLKVKPILHFDNKVIVPFEKIRTRKKAISRIYELLDEDASKGLPMRAAVIHANREEEAAKIIEELSAKYPHVEFYNSYFGAVIGTHLGEGALGICWCFK 281
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
   Legend:   → Mismatch (orange background)
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  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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DEGV_BACSU | P32436)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.

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