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- PDB-2vi3: Atomic resolution (0.98 A) structure of purified thaumatin I grow... -

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Basic information

Entry
Database: PDB / ID: 2vi3
TitleAtomic resolution (0.98 A) structure of purified thaumatin I grown in sodium DL-tartrate at 20 C
ComponentsTHAUMATIN-1
KeywordsPLANT PROTEIN / KINETICS OF CRYSTALLIZATION / CHIRALITY / TEMPERATURE / MICROBATCH / SWEET 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsJakoncic, J. / Asherie, N. / Ginsberg, C.
CitationJournal: Cryst.Growth Des. / Year: 2009
Title: Tartrate Chirality Determines Thaumatin Crystal Habit
Authors: Asherie, N. / Jakoncic, J. / Ginsberg, C. / Greenbaum, A. / Stojanoff, V. / Hrnjez, B.J. / Blass, S. / Berger, J.
History
DepositionNov 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6535
Polymers22,2271
Non-polymers4264
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.849, 57.849, 149.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein THAUMATIN-1 / THAUMATIN / THAUMATIN I


Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM ARIL COVERING SEEDS / Source: (natural) 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 42.8 % / Description: NONE
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.1
Details: MICROBATCH METHOD; PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM DL-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 20 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8209
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 24, 2007 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8209 Å / Relative weight: 1
ReflectionResolution: 0.98→20 Å / Num. obs: 145126 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 37.8
Reflection shellResolution: 0.98→1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KWN

1kwn
PDB Unreleased entry


Resolution: 0.98→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.359 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.134 7256 5 %RANDOM
Rwork0.124 ---
obs0.125 137762 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 0.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 28 353 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221783
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9682445
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7385254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25922.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.35115292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2611519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021414
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.2924
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21234
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3511.51129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98521799
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4063742
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2194.5624
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.98→1.01 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.195 524
Rwork0.193 10019

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