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

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Basic information

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


defense response / cytoplasmic vesicle / extracellular region
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: 1.75 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THAUMATIN ISOFORM A


Theoretical massNumber of molelcules
Total (without water)22,2281
Polymers22,2281
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.300, 63.700, 72.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 84

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Components

#1: Protein THAUMATIN ISOFORM A


Mass: 22228.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
Common name: PEG3350

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Data collection

Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 46816 / % possible obs: 89.3 % / Num. measured all: 254087 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.72 Å / % possible obs: 68.2 % / Num. unique obs: 6977 / Num. measured obs: 11337 / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 1.56

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.75→12 Å / σ(F): 3 /
RfactorNum. reflection
obs0.165 19668
Refinement stepCycle: LAST / Resolution: 1.75→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 0 123 1674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.93
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 all: 0.215 / Rfactor obs: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.15 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d2.93
X-RAY DIFFRACTIONt_dihedral_angle_d18.34
X-RAY DIFFRACTIONt_dihedral_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.019
X-RAY DIFFRACTIONt_chiral_restr0

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