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(-) Description

Title :  ATOMIC RESOLUTION (0.95 A) STRUCTURE OF PURIFIED THAUMATIN I GROWN IN SODIUM MESO-TARTRATE AT 19 C.
 
Authors :  J. Jakoncic, N. Asherie, C. Ginsberg
Date :  21 May 08  (Deposition) - 14 Jul 09  (Release) - 24 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Dl-Tartaric Acid, Cytoplasmic Vesicle, Taste-Modifying Protein, Chirality, Microbatch, Temperature, Sweet Protein, Plant Protein, Crystallization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Asherie, J. Jakoncic, C. Ginsberg, A. Greenbaum, V. Stojanoff, B. J. Hrnjez, S. Blass, J. Berger
Tartrate Chirality Determines Thaumatin Crystal Habit
Cryst. Growth Des. V. 9 4189 2009
PubMed: search  |  Reference-DOI: 10.1021/CG900465H

(-) Compounds

Molecule 1 - THAUMATIN-1
    Chains: A
    Organism Common: KATEMFE
    Organism Scientific: THAUMATOCOCCUS DANIELLII
    Organism Taxid: 4621
    Other Details: FROM ARIL
    Synonym: THAUMATIN 1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:14 , ASP A:55 , CYS A:56 , TYR A:57 , ALA A:128 , ASP A:129 , GLN A:133 , LEU A:176 , GOL A:1209 , HOH A:2123 , HOH A:2230 , HOH A:2334BINDING SITE FOR RESIDUE GOL A1208
2AC2SOFTWAREGLY A:44 , ASN A:46 , TYR A:57 , GLN A:94 , ALA A:128 , GOL A:1208 , HOH A:2335 , HOH A:2336 , HOH A:2337BINDING SITE FOR RESIDUE GOL A1209
3AC3SOFTWAREALA A:1 , ASN A:40 , GLU A:42 , ARG A:82 , HOH A:2339 , HOH A:2340 , HOH A:2341BINDING SITE FOR RESIDUE GOL A1210

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:9 -A:204
2A:56 -A:66
3A:71 -A:77
4A:121 -A:193
5A:126 -A:177
6A:134 -A:145
7A:149 -A:158

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:83 -Pro A:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VU6)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THAUMATIN_2PS51367 Thaumatin family profile.THM1_THADA1-207  1A:1-207
2THAUMATIN_1PS00316 Thaumatin family signature.THM1_THADA62-77  1A:62-77

(-) Exons   (0, 0)

(no "Exon" information available for 2VU6)

(-) 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:207
 aligned with THM1_THADA | P02883 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           THM1_THADA     1 ATFEIVNRCSYTVWAAASKGDAALDAGGRQLNSGESWTINVEPGTNGGKIWARTDCYFDDSGSGICKTGDCGGLLRCKRFGRPPTTLAEFSLNQYGKDYIDISNIKGFNVPMNFSPTTRGCRGVRCAADIVGQCPAKLKAPGGGCNDACTVFQTSEYCCTTGKCGPTEYSRFFKRLCPDAFSYVLDKPTTVTCPGSSNYRVTFCPTA 207
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vu6A00 A:1-207 Thaumatin                                                                                                                                                                                       CATH domains
               Pfam domains ------Thaumatin-2vu6A01 A:7-205                                                                                                                                                                              -- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee....eeeeeeeee....eeeee.......eeeeeeeeeee.....eeeee..................eeeeeeee..eeeeeee........eeeee.......eee..hhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhh.....................eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THAUMATIN_2  PDB: A:1-207 UniProt: 1-207                                                                                                                                                                        PROSITE (1)
                PROSITE (2) -------------------------------------------------------------THAUMATIN_1     ---------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vu6 A   1 ATFEIVNRCSYTVWAAASKGDAALDAGGRQLNSGESWTINVEPGTNGGKIWARTDCYFDDSGSGICKTGDCGGLLRCKRFGRPPTTLAEFSLNQYGKDYIDISNIKGFNVPMNFSPTTRGCRGVRCAADIVGQCPAKLKAPGGGCNDACTVFQTSEYCCTTGKCGPTEYSRFFKRLCPDAFSYVLDKPTTVTCPGSSNYRVTFCPTA 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 2VU6)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Thaumatin] (24)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (THM1_THADA | P02883)
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.

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  2vu6
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  THM1_THADA | P02883
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 Related Entries

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

UniProtKB/Swiss-Prot
        THM1_THADA | P02883: 1kwn 1lr2 1lr3 1lxz 1ly0 1pp3 1rqw 1thi 1thu 1thv 1thw 2a7i 2blr 2blu 2d8o 2d8p 2g4y 2oqn 2pe7 2vhk 2vhr 2vi1 2vi2 2vi3 2vi4 2vu7 2wbz 3al7 3ald 3dzn 3dzp 3dzr 3e0a 3e3s 3n02 3n03 3qy5 3v7v 3v82 3v84 3v87 3v88 3v8a 3vce 3vcg 3vch 3vci 3vcj 3vck 3vhf 3vhg 3vjq 3x3o 3x3p 3x3q 3x3r 3x3s 3x3t 3zej 4axr 4axu 4bal 4bar 4c3c 4dc5 4dc6 4diy 4diz 4dj0 4dj1 4ek0 4eka 4ekb 4ekh 4eko 4ekt 4el2 4el3 4el7 4ela 4tvt 4xvb 4zg3 4zxr 5a47 5amz 5avg 5fgt 5fgx 5jvx 5k7q 5kvw 5kvx 5kvz 5kw0 5kw3 5kw4 5kw5 5kw7 5kw8 5l4r 5lh0 5lh1 5lh3 5lh5 5lh6 5lh7 5lmh 5ln0 5t3g

(-) Related Entries Specified in the PDB File

1kwn 1.2 A STRUCTURE OF THAUMATIN CRYSTALLIZED IN GEL
1lr2 CRYSTAL STRUCTURE OF THAUMATIN AT HIGH HYDROSTATIC PRESSURE
1lr3 CRYSTAL STRUCTURE OF THAUMATIN AT HIGH HYDROSTATIC PRESSURE
1lxz STRUCTURE OF THAUMATIN CRYSTALLIZED IN THE PRESENCE OFGLYCEROL
1ly0 STRUCTURE OF THAUMATIN CRYSTALLIZED IN THE PRESENCE OFGLYCEROL
1pp3 STRUCTURE OF THAUMATIN IN A HEXAGONAL SPACE GROUP
1rqw THAUMATIN STRUCTURE AT 1.05 A RESOLUTION
1thi THAUMATIN I
1thu THAUMATIN ISOFORM B (MONOCLINIC CRYSTAL FORM)
1thv THAUMATIN ISOFORM A (ORTHORHOMBIC CRYSTAL FORM)
1thw THAUMATIN (TETRAGONAL CRYSTAL FORM)
2a7i ON THE ROUTINE USE OF SOFT X-RAYS IN MACROMOLECULARCRYSTALLOGRAPHY, PART III- THE OPTIMAL DATA COLLECTIONWAVELENGTH
2blr THAUMATIN BEFORE A HIGH DOSE X-RAY "BURN"
2blu THAUMATIN AFTER A HIGH DOSE X-RAY "BURN"
2d8o STRUCTURE OF VIL-THAUMATIN
2d8p STRUCTURE OF HYPER-VIL-THAUMATIN
2vhk ATOMIC RESOLUTION (0.94 A) STRUCTURE OF PURIFIED THAUMATIN I GROWN IN SODIUM L- TARTRATE AT 22C
2vhr ATOMIC RESOLUTION (0.95A) STRUCTURE OF PURIFIED THAUMATIN I GROWN IN SODIUM L- TARTRATE AT 4 C
2vi1 ATOMIC RESOLUTION (1.04 A) STRUCTURE OF PURIFIED THAUMATIN I GROWN IN SODIUM D- TARTRATE AT 22 C.
2vi2 ATOMIC RESOLUTION (1.05 A) STRUCTURE OF PURIFIED THAUMATIN I GROWN IN SODIUM D- TARTRATE AT 4C
2vi3 ATOMIC RESOLUTION (0.98 A) STRUCTURE OF PURIFIED THAUMATIN I GROWN IN SODIUM DL- TARTRATE AT 20 C
2vi4 ATOMIC RESOLUTION (1.10 A) STRUCTURE OF PURIFIED THAUMATIN I GROWN IN SODIUM DL- TARTRATE AT 6 C.
2vu7 ATOMIC RESOLUTION (1.08 A) STRUCTURE OF PURIFIED THAUMATIN I GROWN IN SODIUM MESO- TARTRATE AT 4 C