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- PDB-1thu: THE STRUCTURES OF THREE CRYSTAL FORMS OF THE SWEET PROTEIN THAUMATIN -

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Basic information

Entry
Database: PDB / ID: 1thu
TitleTHE STRUCTURES OF THREE CRYSTAL FORMS OF THE SWEET PROTEIN THAUMATIN
ComponentsTHAUMATIN ISOFORM B
KeywordsSWEET TASTING PROTEIN
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsKo, T.-P. / Day, J. / Greenwood, A. / McPherson, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Structures of three crystal forms of the sweet protein thaumatin.
Authors: Ko, T.P. / Day, J. / Greenwood, A. / McPherson, A.
History
DepositionJun 10, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THAUMATIN ISOFORM B


Theoretical massNumber of molelcules
Total (without water)22,2431
Polymers22,2431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.700, 44.900, 38.000
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO 84

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Components

#1: Protein THAUMATIN ISOFORM B


Mass: 22243.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
Has protein modificationY
Sequence detailsCROSS REFERENCE TO SEQUENCE DATABASE SWISS-PROT ENTRY NAME PDB ENTRY CHAIN NAME THM1_THADA SEQUENCE ...CROSS REFERENCE TO SEQUENCE DATABASE SWISS-PROT ENTRY NAME PDB ENTRY CHAIN NAME THM1_THADA SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: THM1_THADA SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASN 56 LYS 56 ASN 113 ASP 113

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
Common name: PEG3350

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Data collection

Reflection
*PLUS
Highest resolution: 2.61 Å / Num. obs: 8350 / % possible obs: 70.8 % / Num. measured all: 27736 / Rmerge(I) obs: 0.1062
Reflection shell
*PLUS
Highest resolution: 2.61 Å / Lowest resolution: 2.81 Å / % possible obs: 38.1 % / Num. unique obs: 892 / Num. measured obs: 1854 / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.84

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.6→8 Å / σ(F): 3 /
RfactorNum. reflection
obs0.184 4622
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 0 0 1552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg2.95
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.76 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_d21.81
X-RAY DIFFRACTIONt_plane_restr0.02
X-RAY DIFFRACTIONt_chiral_restr0
X-RAY DIFFRACTIONt_angle_deg2.954

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