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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT NITROBINDIN M75L/H76L/Q96C/M148L/H158L (NB4) FROM ARABIDOPSIS THALIANA
 
Authors :  E. Mizohata, K. Fukumoto, A. Onoda, M. Bocola, M. Arlt, T. Inoue, U. Schw T. Hayashi
Date :  08 Oct 13  (Deposition) - 09 Apr 14  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Barrel, Intracellular Transport, Hydrophobic Ligands, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Fukumoto, A. Onoda, E. Mizohata, M. Bocola, T. Inoue, U. Schwaneberg, T. Hayashi
A Rhodium Complex-Linked Hybrid Biocatalyst: Stereo-Controlled Phenylacetylene Polymerization Within An Engineered Protein Cavity
Chemcatchem 2014
PubMed: search  |  Reference-DOI: 10.1002/CCTC.201301055

(-) Compounds

Molecule 1 - UPF0678 FATTY ACID-BINDING PROTEIN-LIKE PROTEIN AT1G79260
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET42B(+)
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT1G79260, AT1G79260.1, YUP8H12R.14
    Mutation: YES
    Organism Common: MOUSE-EAR CRESS, THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: NITROBINDIN

 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
1BA4Ligand/IonBARIUM ION
2P6G2Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:86 , HOH A:616 , HOH A:634 , HOH A:647BINDING SITE FOR RESIDUE BA A 501
2AC2SOFTWAREGLU A:112 , GLU A:136 , LEU A:137 , HOH A:673 , ASP B:111BINDING SITE FOR RESIDUE BA A 502
3AC3SOFTWAREPHE A:44 , LEU A:76BINDING SITE FOR RESIDUE P6G A 503
4AC4SOFTWAREPRO B:86BINDING SITE FOR RESIDUE BA B 501
5AC5SOFTWAREASP A:111 , GLU B:112 , GLU B:136 , LEU B:137 , HOH B:625BINDING SITE FOR RESIDUE BA B 502
6AC6SOFTWARETHR B:66 , LEU B:76 , HOH B:602BINDING SITE FOR RESIDUE P6G B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:71 -Gly B:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WJB)

(-) 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:153
 aligned with Y1926_ARATH | O64527 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:153
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163   
          Y1926_ARATH    14 PPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAYTQKTWKLESGAPMHAESGYFRPRPDGSIEVVIAQSTGLVEVQKGTYNVDEQSIKLKSDLVGNASKVKEISREFELVDGKLSYVVRMSTTTNPLQPHLKAILDKL 166
               SCOP domains d3wjba_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhheeeeeeeee.........eeeeeeeee.....eeeeeeee......eeeeeeeeeee....eeeeeeee...eeeeeeeeee....eeeeeeeeee....eeeeeeeeeee..eeeeeeeeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wjb A  14 PPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAYTQKTWKLESGAPLLAESGYFRPRPDGSIEVVIACSTGLVEVQKGTYNVDEQSIKLKSDLVGNASKVKEISREFELVDGKLSYVVRLSTTTNPLQPLLKAILDKL 166
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163   


Chain B from PDB  Type:PROTEIN  Length:153
 aligned with Y1926_ARATH | O64527 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:153
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163   
          Y1926_ARATH    14 PPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAYTQKTWKLESGAPMHAESGYFRPRPDGSIEVVIAQSTGLVEVQKGTYNVDEQSIKLKSDLVGNASKVKEISREFELVDGKLSYVVRMSTTTNPLQPHLKAILDKL 166
               SCOP domains d3wjbb_ B: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh...eeeeeeeeeee..eeeeeeeeeeeee......eeeeeeeee.....eeeeeeeeeee....eeeeeeee....eeeeeee........eeeeeeee....eeeeeeeeeee..eeeeeeeeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wjb B  14 PPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAYTQKTWKLESGAPLLAESGYFRPRPDGSIEVVIACSTGLVEVQKGTYNVDEQSIKLKSDLVGNASKVKEISREFELVDGKLSYVVRLSTTTNPLQPLLKAILDKL 166
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Y1926_ARATH | O64527)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  Cis Peptide Bonds
    Ser B:71 - Gly B:72   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        Y1926_ARATH | O64527: 2a13 2q4n 3emm 3wjc 3wjd 3wje 3wjf 3wjg 4ymy

(-) Related Entries Specified in the PDB File

3wjb 3wjc 3wjd 3wje 3wjg