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

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Basic information

Entry
Database: PDB / ID: 1thw
TitleTHE STRUCTURES OF THREE CRYSTAL FORMS OF THE SWEET PROTEIN THAUMATIN
ComponentsTHAUMATIN
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
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3932
Polymers22,2431
Non-polymers1501
Water1,892105
1
A: THAUMATIN
hetero molecules

A: THAUMATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7864
Polymers44,4862
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)58.600, 58.600, 151.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: CIS PROLINE - PRO 84

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Components

#1: Protein THAUMATIN


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
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlthaumatin1drop
21 Msodium potassium tartrate1reservoir
30.1 Msodium-N-2-acetamido-iminodiacetic acid1reservoir

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.75→12 Å / σ(F): 3 /
RfactorNum. reflection
obs0.181 25864
Refinement stepCycle: LAST / Resolution: 1.75→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 10 105 1667
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 obs: 0.181 / Rfactor all: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.92 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d2.93
X-RAY DIFFRACTIONt_dihedral_angle_d18.08
X-RAY DIFFRACTIONt_dihedral_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.019
X-RAY DIFFRACTIONt_chiral_restr0
LS refinement shell
*PLUS
Lowest resolution: 1.779 Å / Num. reflection obs: 723 / Rfactor obs: 0.181

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